9pis

Ab initio structure of crambin by MicroED at 0.85A

Method: ELECTRON CRYSTALLOGRAPHY Dmax: 35.8 Å Quality: GOOD

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

Crambin

OrganismNot specified

UniProt P01542

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–46 Not recorded No other associated polymer ELECTRON CRYSTALLOGRAPHY cryo-EM buffer:pH 7;Simple mixture of ethanol and water. cryo-EM vitrification conditions:Cryogen ETHANE Resolution 0.85 Å R-free 0.164

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.

26 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CRAM_CRAAB
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–46; UniProt 1–46

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9pis

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9pis
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9pis
Deposition date deposition_date2025-07-11
Structure title titleAb initio structure of crambin by MicroED at 0.85A
Keywords keywordsSeed protein, PLANT PROTEIN; PLANT PROTEIN
Experimental Method methodELECTRON CRYSTALLOGRAPHY

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

Radius of gyration Rg (Guinier) rg_guinier10.57
Radius of gyration Rg (electron density) rg_electron9.72
Forward intensity I(0) i0606875.00
Molecular weight molecular_weight4709.0 kDa
Excluded volume excluded_volume5771 ų
Envelope volume envelope_volume6209 ų
Hydration-shell volume shell_volume5926 ų
Envelope diameter envelope_diameter32.2
Shell Rg shell_rg14.42
Envelope Rg envelope_rg10.05
Shape Rg shape_rg9.74
Total Rg total_rg11.04
Total atoms total_atoms638
Residues n_residues46
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax35.8
Rg (real space) rg_real10.56
Rg uncertainty (real space) rg_real_error0.29
I(0) (real space) i0_real6.0690e+05
I(0) uncertainty (real space) i0_real_error5.9700e+03
Rg (reciprocal space) rg_reciprocal10.56
I(0) (reciprocal space) i0_reciprocal606900.0000
Solution quality estimate total_estimate0.8808
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary12.2
Skewness Skewness skewness0.305
Kurtosis Kurtosis kurtosis-0.239
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha77250.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.972

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (2)

9. Files and Curves (10)