SAXSdb — 1c04

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1. Protein Identity and Related Structures Protein Identity & Related Structures

RIBOSOMAL PROTEIN L2

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 4 RNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 60–196	Fragment：CENTRAL RNA-BINDING DOMAINS Non-standard monomer：Yes (specific site not provided by mmCIF)	23S RRNA FRAGMENT × 1 23S RRNA FRAGMENT × 1 RIBOSOMAL PROTEIN L6 × 1 （P02391） RIBOSOMAL PROTEIN L11 × 1 （P56210） RIBOSOMAL PROTEIN L14 × 1 （P04450）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.4；292 K；PEG 6000, POTASSIUM CHLORIDE, AMMONIUM CHLORIDE, MAGNESIUM CHLORIDE, ACETATE, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 5.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1C04	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1RL2 RIBOSOMAL PROTEIN L2 RNA-BINDING DOMAIN FROM BACILLUS STEAROTHERMOPHILUS Deposited 1999-03-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 60–196（137 aa）	Mutation：METHIONINES ARE SUBSTITUED BY SELONOMETHIONINE Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 15% PEK20000 IN 0.1M MES PH6, pH 6.5	Resolution 2.30 Å R-free 0.258
1RL2 RIBOSOMAL PROTEIN L2 RNA-BINDING DOMAIN FROM BACILLUS STEAROTHERMOPHILUS Deposited 1999-03-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 60–196（137 aa）	Mutation：METHIONINES ARE SUBSTITUED BY SELONOMETHIONINE Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 15% PEK20000 IN 0.1M MES PH6, pH 6.5	Resolution 2.30 Å R-free 0.258
487D SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION Deposited 2000-02-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain I 61–195（135 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 7.50 Å
4V42 Crystal structure of the ribosome at 5.5 A resolution. Deposited 2001-03-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 49-meric	Chain BD 60–196（137 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 5.50 Å

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL2_BACST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–137； UniProt 60–196

RIBOSOMAL PROTEIN L6

OrganismNot specified

UniProt P02391

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 4 RNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain B； UniProt 1–177	Not recorded	23S RRNA FRAGMENT × 1 23S RRNA FRAGMENT × 1 RIBOSOMAL PROTEIN L2 × 1 （P04257） RIBOSOMAL PROTEIN L11 × 1 （P56210） RIBOSOMAL PROTEIN L14 × 1 （P04450）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.4；292 K；PEG 6000, POTASSIUM CHLORIDE, AMMONIUM CHLORIDE, MAGNESIUM CHLORIDE, ACETATE, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 5.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1C04	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EG0 FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME Deposited 2000-02-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: pentadecameric	Chain J 1–171（171 aa）	Mutation：B. STEAROTHERMOPHILUS SEQUENCE AND MODEL	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM Hepes, 6 mM Mg(CH3COO)2 150 mM NH4Cl, 4 mM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.50 Å
1RL6 RIBOSOMAL PROTEIN L6 Deposited 1999-01-14	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–177（177 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；pH 7.6	Resolution 2.00 Å R-free 0.302
487D SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION Deposited 2000-02-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain J 8–171（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 7.50 Å
4V42 Crystal structure of the ribosome at 5.5 A resolution. Deposited 2001-03-30	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 49-meric	Chain BH 1–177（177 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 5.50 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL6_BACST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–177； UniProt 1–177

RIBOSOMAL PROTEIN L11

OrganismNot specified

UniProt P56210

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 4 RNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain C； UniProt 63–129	Fragment：C-TERMINAL DOMAIN	23S RRNA FRAGMENT × 1 23S RRNA FRAGMENT × 1 RIBOSOMAL PROTEIN L2 × 1 （P04257） RIBOSOMAL PROTEIN L6 × 1 （P02391） RIBOSOMAL PROTEIN L14 × 1 （P04450）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.4；292 K；PEG 6000, POTASSIUM CHLORIDE, AMMONIUM CHLORIDE, MAGNESIUM CHLORIDE, ACETATE, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 5.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1C04	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ACI L11 RIBOSOMAL PROTEIN RNA BINDING DOMAIN, NMR, 20 STRUCTURES Deposited 1997-02-07	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–133（75 aa） Fragment：C-TERMINAL DOMAIN, 76 RESIDUES	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K	Resolution not provided
1FOW NMR STRUCTURE OF L11-C76, THE C-TERMINAL DOMAIN OF 50S RIBOSOMAL PROTEIN L11, MINIMIZED AVERAGE STRUCTURE Deposited 1996-09-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–133（75 aa） Fragment：CARBOXYL-TERMINAL DOMAIN OF PROTEIN L11, RESIDUES THR 59 TO ASP 133	Mutation：INS(MET1)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；298 K	Resolution not provided
1FOX NMR STRUCTURE OF L11-C76, THE C-TERMINAL DOMAIN OF 50S RIBOSOMAL PROTEIN L11, 33 STRUCTURES Deposited 1996-09-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–133（75 aa） Fragment：CARBOXYL-TERMINAL DOMAIN OF PROTEIN L11, RESIDUES THR 59 TO ASP 133	Mutation：INS(MET1)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；298 K	Resolution not provided
1FOY THE RNA BINDING DOMAIN OF RIBOSOMAL PROTEIN L11: THREE-DIMENSIONAL STRUCTURE OF THE RNA-BOUND FORM OF THE PROTEIN, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-05-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–133（75 aa） Fragment：C-TERMINAL DOMAIN, 75 RESIDUES	Mutation：F1M	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；320 K	Resolution not provided
1HC8 CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX Deposited 2001-04-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 58–133（76 aa） Fragment：C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11	Not recorded	MG MAGNESIUM ION × 10 K POTASSIUM ION × 1 OS OSMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PEG 600, MAGNESIUM ACETATE, COBALT HEXAMINE CHLORIDE, SODIUM CACODYLATE, KCL, pH 6.50	Resolution 2.80 Å R-free 0.253
1HC8 CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX Deposited 2001-04-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 58–133（76 aa） Fragment：C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11	Not recorded	MG MAGNESIUM ION × 11 K POTASSIUM ION × 1 OS OSMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PEG 600, MAGNESIUM ACETATE, COBALT HEXAMINE CHLORIDE, SODIUM CACODYLATE, KCL, pH 6.50	Resolution 2.80 Å R-free 0.253
1QA6 CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX Deposited 1999-04-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 63–129（67 aa） Fragment：C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11	Not recorded	MG MAGNESIUM ION × 2 OS OSMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；310 K；PEG 600, MAGNESIUM ACETATE, COBALT HEXAMINE CHLORIDE, SODIUM CACODYLATE, KCL, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 310.00K	Resolution 2.80 Å R-free 0.321
1QA6 CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX Deposited 1999-04-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 63–129（67 aa） Fragment：C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11	Not recorded	MG MAGNESIUM ION × 2 OS OSMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；310 K；PEG 600, MAGNESIUM ACETATE, COBALT HEXAMINE CHLORIDE, SODIUM CACODYLATE, KCL, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 310.00K	Resolution 2.80 Å R-free 0.321
1Y39 Co-evolution of protein and RNA structures within a highly conserved ribosomal domain Deposited 2004-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 58–133（76 aa） Fragment：C-Terminal Domain Of Ribosomal Protein L11	Mutation：S69N	3CO COBALT (III) ION × 1 K POTASSIUM ION × 1 MG MAGNESIUM ION × 10 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；310 K；PEG600, Magnesium acetate, glycerol, sodium cacodylate, potasium chlroride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K	Resolution 2.80 Å R-free 0.253
1Y39 Co-evolution of protein and RNA structures within a highly conserved ribosomal domain Deposited 2004-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 58–133（76 aa） Fragment：C-Terminal Domain Of Ribosomal Protein L11	Mutation：S69N	3CO COBALT (III) ION × 1 K POTASSIUM ION × 1 MG MAGNESIUM ION × 8 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；310 K；PEG600, Magnesium acetate, glycerol, sodium cacodylate, potasium chlroride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K	Resolution 2.80 Å R-free 0.253
2FOW THE RNA BINDING DOMAIN OF RIBOSOMAL PROTEIN L11: THREE-DIMENSIONAL STRUCTURE OF THE RNA-BOUND FORM OF THE PROTEIN, NMR, 26 STRUCTURES Deposited 1997-05-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–133（75 aa） Fragment：C-TERMINAL DOMAIN, 75 RESIDUES	Mutation：F1M	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；320 K	Resolution not provided

8 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL11_BACST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain C； PDBConstruct 1–67； UniProt 63–129

RIBOSOMAL PROTEIN L14

OrganismNot specified

UniProt P04450

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 4 RNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain D； UniProt 1–122	Not recorded	23S RRNA FRAGMENT × 1 23S RRNA FRAGMENT × 1 RIBOSOMAL PROTEIN L2 × 1 （P04257） RIBOSOMAL PROTEIN L6 × 1 （P02391） RIBOSOMAL PROTEIN L11 × 1 （P56210）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.4；292 K；PEG 6000, POTASSIUM CHLORIDE, AMMONIUM CHLORIDE, MAGNESIUM CHLORIDE, ACETATE, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 5.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1C04	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WHI RIBOSOMAL PROTEIN L14 Deposited 1996-01-10	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.50 Å R-free 0.255
487D SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION Deposited 2000-02-23	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain M 1–122（122 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 7.50 Å
4V42 Crystal structure of the ribosome at 5.5 A resolution. Deposited 2001-03-30	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 49-meric	Chain BN 1–122（122 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 5.50 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL14_BACST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain D； PDBConstruct 1–122； UniProt 1–122

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1c04
Deposition date deposition_date	1999-07-14
Structure title title	IDENTIFICATION OF KNOWN PROTEIN AND RNA STRUCTURES IN A 5 A MAP OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA MARISMORTUI
Keywords keywords	LOW RESOLUTION MODEL, LARGE RIBOSOME UNIT, RIBOSOME; RIBOSOME
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	58.51 Å
Radius of gyration Rg (electron density) rg_electron	64.80 Å
Forward intensity I(0) i0	153885000.00
Molecular weight molecular_weight	81179.0 kDa
Excluded volume excluded_volume	92874 Å³
Envelope volume envelope_volume	198120 Å³
Hydration-shell volume shell_volume	30972 Å³
Envelope diameter envelope_diameter	202.3 Å
Shell Rg shell_rg	52.11 Å
Envelope Rg envelope_rg	62.69 Å
Shape Rg shape_rg	64.80 Å
Total Rg total_rg	64.38 Å
Total atoms total_atoms	5570
Residues n_residues	572
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	119.0 Å
Rg (real space) rg_real	42.39 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	1.3040e+08
I(0) uncertainty (real space) i0_real_error	2.0980e+06
Rg (reciprocal space) rg_reciprocal	56.82 Å
I(0) (reciprocal space) i0_reciprocal	153000000.0000
Solution quality estimate total_estimate	0.5749
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	30.8 Å
Skewness Skewness skewness	0.229
Kurtosis Kurtosis kurtosis	-0.924
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	1.2640
Highest regularization parameter α highest_alpha	1450000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.020; Oscil: 0.972; Stabil: 0.966; Sysdev: 0.000; Positv: 1.000; Valcen: 0.659; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	23S RRNA FRAGMENT
Molecular weight formula_weight	18725.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E
Atom count atom_count	5570

GCCAGGAUGUAGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGU

Entity 2 Entity 2 polymer

Description description	23S RRNA FRAGMENT
Molecular weight formula_weight	9376.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	F

GGGUGCUCAGUACGAGAGGAACCGCACCC

Entity 3 Entity 3 polymer

Description description	RIBOSOMAL PROTEIN L2
Molecular weight formula_weight	14930.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

QYRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYIIAPKNLKVGMEIMSGPDADIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLASGEVRMILGKCRATVGEVGN

Entity 4 Entity 4 polymer

Description description	RIBOSOMAL PROTEIN L6
Molecular weight formula_weight	19202.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SRVGKKPIEIPAGVTVTVNGNTVTVKGPKGELTRTFHPDMTITVEGNVITVTRPSDEKHHRALHGTTRSLLANMVEGVSKGYEKALELVGVGYRASKQGKKLVLSVGYSHPVEIEPEEGLEIEVPSQTKIIVKGADKQRVGELAANIRAVRPPEPYKGKGIRYEGELVRLKEGKTGK

Entity 5 Entity 5 polymer

Description description	RIBOSOMAL PROTEIN L11
Molecular weight formula_weight	7116.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

KTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARSMGI

Entity 6 Entity 6 polymer

Description description	RIBOSOMAL PROTEIN L14
Molecular weight formula_weight	13369.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MIQQESRLKVADNSGAREVLVIKVLGGSGRRYANIGDVVVATVKDATPGGVVKKGQVVKAVVVRTKRGVRRPDGSYIRFDENACVIIRDDKSPRGTRIFGPVARELRDKDFMKIISLAPEVI

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1c04a_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d1c04b_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d1c04c_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d1c04d_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

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8. Citations (2)

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Unit-cell length a length_a	212.000 Å
Unit-cell length b length_b	301.400 Å
Unit-cell length c length_c	576.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	5.000 Å
Low-resolution limit resolution_low	60.000 Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/c0/1c04/1c04.fit
pddf	/app/data/pr_computation/c0/1c04/1c04.pr.out
profile	/app/data/saxs_computation/c0/1c04/1c04.dat

IDENTIFICATION OF KNOWN PROTEIN AND RNA STRUCTURES IN A 5 A MAP OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA MARISMORTUI

1. Protein Identity and Related Structures Protein Identity & Related Structures

RIBOSOMAL PROTEIN L2

State in the Current Structure

Other States of the Same Protein in the Database

RIBOSOMAL PROTEIN L6

State in the Current Structure

Other States of the Same Protein in the Database

RIBOSOMAL PROTEIN L11

State in the Current Structure

Other States of the Same Protein in the Database

RIBOSOMAL PROTEIN L14

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)