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9s39

Serial crystallography structure of a photosynthetic reaction center using a goniometer-compatible 96-well chip-based platform

Method: X-RAY DIFFRACTION D_max: 128.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s39
deposition_date	2025-07-24
last_revision	2026-06-10
title	Serial crystallography structure of a photosynthetic reaction center using a goniometer-compatible 96-well chip-based platform
keywords	Reaction center blastochloris viridis structure, PHOTOSYNTHESIS; PHOTOSYNTHESIS
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	36.82 Å
rg_electron	35.90 Å
i0	261667000.00
molecular_weight	141050.0 kDa
excluded_volume	180040 Å³
envelope_volume	211800 Å³
shell_volume	49866 Å³
envelope_diameter	134.1 Å
shell_rg	41.58 Å
envelope_rg	36.28 Å
shape_rg	35.83 Å
total_rg	36.55 Å
total_atoms	19335
n_residues	1177
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	128.0 Å
rg_real	37.07 Å
rg_real_error	1.49 Å
i0_real	2.6170e+08
i0_real_error	4.4680e+06
rg_reciprocal	36.92 Å
i0_reciprocal	261600000.0000
total_estimate	0.8385
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	35.7 Å
skewness	0.539
kurtosis	-0.138
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	45830000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.774; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.845; Smooth: 0.731

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4. Crystallography & Experiment

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5. Entities & Polymer Info (13)

Entity 1 polymer

description	Photosynthetic reaction center cytochrome c subunit
formula_weight	37108.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C
atom_count	19384

CFEPPPATTTQTGFRGLSMGEVLHPATVKAKKERDAQYPPALAAVKAEGPPVSQVYKNVKVLGNLTEAEFLRTMTAITEWVSPQEGCTYCHDENNLASEAKYPYVVARRMLEMTRAINTNWTQHVAQTGVTCYTCHRGTPLPPYVRYLEPTLPLNNRETPTHVERVETRSGYVVRLAKYTAYSALNYDPFTMFLANDKRQVRVVPQTALPLVGVSRGKERRPLSDAYATFALMMSISDSLGTNCTFCHNAQTFESWGKKSTPQRAIAWWGIRMVRDLNMNYLAPLNASLPASRLGRQGEAPQADCRTCHQGVTKPLFGASRLKDYPELGPIK

Entity 2 polymer

description	Reaction center protein H chain
formula_weight	26863.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

HLDIAQLVWYAQWLVIWTVVLLYLRREDRREGYPLVEPEDGQVYELPYPKTFVLPHGGTVTVPRRRPETRELKLAQTDGFEGAPLQPTGNPLVDAVGPASYAERAEVVDATVDGKAKIVPLRVATDFSIAEGDVDPRGLPVVAADGVEAGTVTDLWVDRSEHYFRYLELSVAGSARTALIPLGFCDVKKDKIVVTSILSEQFANVPRLQSRDQITLREEDKVSAYYAGGLLYATPERAESLL

Entity 3 polymer

description	Reaction center protein L chain
formula_weight	30469.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNIFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS

Entity 4 polymer

description	Reaction center protein M chain
formula_weight	35932.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M

ADYQTIYTQIQARGPHITVSGEWGDNDRVGKPFYSYWLGKIGDAQIGPIYLGASGIAAFAFGSTAILIILFNMAAEVHFDPLQFFRQFFWLGLYPPKAQYGMGIPPLHDGGWWLMAGLFMTLSLGSWWIRVYSRARALGLGTHIAWNFAAAIFFVLCIGCIHPTLVGSWSEGVPFGIWPHIDWLTAFSIRYGNFYYCPWHGFSIGFAYGCGLLFAAHGATILAVARFGGDREIEQITDRGTAVERAALFWRWTIGFNATIESVHRWGWFFSLMVMVSASVGILLTGTFVDNWYLWCVKHGAAPDYPAYLPATPDPASLPGAPK

Entity 5 polymer

description	FME-TYR-HIS-GLY-ALA-LEU-ALA-GLN
formula_weight	919.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MYHGALAQ

Entity 6 non-polymer

description	HEME C
formula_weight	618.5 kDa
src_method	syn
entity_count	4

Entity 7 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	8

Entity 8 non-polymer

description	BACTERIOCHLOROPHYLL B
formula_weight	909.5 kDa
src_method	syn
entity_count	4

Entity 9 non-polymer

description	BACTERIOPHEOPHYTIN B
formula_weight	887.2 kDa
src_method	syn
entity_count	2

Entity 10 non-polymer

description	FE (II) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	1

Entity 11 non-polymer

description	MENAQUINONE-7
formula_weight	649.0 kDa
src_method	syn
entity_count	1

Entity 12 non-polymer

description	15-cis-1,2-dihydroneurosporene
formula_weight	540.9 kDa
src_method	syn
entity_count	1

Entity 13 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	49

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6. Citations (1)

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length_a	226.500 Å
length_b	226.500 Å
length_c	113.900 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	3.300 Å
resolution_low	60.000 Å
r_factor	—
r_work	0.2462
r_free	0.2963

fit	/app/data/saxs_computation/s3/9s39/9s39.fit
pddf	/app/data/pr_computation/s3/9s39/9s39.pr.out
profile	/app/data/saxs_computation/s3/9s39/9s39.dat

Serial crystallography structure of a photosynthetic reaction center using a goniometer-compatible 96-well chip-based platform

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (13)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

Entity 13 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)