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9vdx

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

Method: X-RAY DIFFRACTION D_max: 125.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vdx
deposition_date	2025-06-09
title	Serial synchrotron crystallography structure of a photosynthetic reaction center using a goniometer-compatible chip-based platform
keywords	Bioenergetics, photosynthesis, serial crystallography, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	37.00 Å
rg_electron	35.94 Å
i0	271392000.00
molecular_weight	145070.0 kDa
excluded_volume	185880 Å³
envelope_volume	218200 Å³
shell_volume	51181 Å³
envelope_diameter	134.2 Å
shell_rg	41.53 Å
envelope_rg	36.45 Å
shape_rg	35.87 Å
total_rg	36.58 Å
total_atoms	10255
n_residues	1185
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	125.8 Å
rg_real	37.24 Å
rg_real_error	1.15 Å
i0_real	2.7140e+08
i0_real_error	4.7870e+06
rg_reciprocal	37.09 Å
i0_reciprocal	271400000.0000
total_estimate	0.8449
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.0 Å
skewness	0.529
kurtosis	-0.142
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	47190000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.887; Smooth: 0.637

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4. Crystallography & Experiment

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5. Entities & Polymer Info (15)

Entity 1 polymer

description	Photosynthetic reaction center cytochrome c subunit
formula_weight	37450.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C
atom_count	10352

CFEPPPATTTQTGFRGLSMGEVLHPATVKAKKERDAQYPPALAAVKAEGPPVSQVYKNVKVLGNLTEAEFLRTMTAITEWVSPQEGCTYCHDENNLASEAKYPYVVARRMLEMTRAINTNWTQHVAQTGVTCYTCHRGTPLPPYVRYLEPTLPLNNRETPTHVERVETRSGYVVRLAKYTAYSALNYDPFTMFLANDKRQVRVVPQTALPLVGVSRGKERRPLSDAYATFALMMSISDSLGTNCTFCHNAQTFESWGKKSTPQRAIAWWGIRMVRDLNMNYLAPLNASLPASRLGRQGEAPQADCRTCHQGVTKPLFGASRLKDYPELGPIKAAAK

Entity 2 polymer

description	Reaction center protein H chain
formula_weight	28557.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MYHGALAQHLDIAQLVWYAQWLVIWTVVLLYLRREDRREGYPLVEPLGLVKLAPEDGQVYELPYPKTFVLPHGGTVTVPRRRPETRELKLAQTDGFEGAPLQPTGNPLVDAVGPASYAERAEVVDATVDGKAKIVPLRVATDFSIAEGDVDPRGLPVVAADGVEAGTVTDLWVDRSEHYFRYLELSVAGSARTALIPLGFCDVKKDKIVVTSILSEQFANVPRLQSRDQITLREEDKVSAYYAGGLLYATPERAESLL

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 non-polymer

description	HEME C
formula_weight	618.5 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	DIACYL GLYCEROL
formula_weight	625.0 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	15

Entity 8 non-polymer

description	LAURYL DIMETHYLAMINE-N-OXIDE
formula_weight	229.4 kDa
src_method	syn
entity_count	7

Entity 9 non-polymer

description	HEPTANE-1,2,3-TRIOL
formula_weight	148.2 kDa
src_method	syn
entity_count	3

Entity 10 non-polymer

description	BACTERIOCHLOROPHYLL B
formula_weight	909.5 kDa
src_method	syn
entity_count	4

Entity 11 non-polymer

description	BACTERIOPHEOPHYTIN B
formula_weight	887.2 kDa
src_method	syn
entity_count	2

Entity 12 non-polymer

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

Entity 13 non-polymer

description	MENAQUINONE-7
formula_weight	649.0 kDa
src_method	syn
entity_count	1

Entity 14 non-polymer

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

Entity 15 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	96

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6. Citations (1)

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length_a	223.800 Å
length_b	223.800 Å
length_c	113.500 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	2.800 Å
resolution_low	36.800 Å
r_factor	—
r_work	0.2150
r_free	0.2530

fit	/app/data/saxs_computation/vd/9vdx/9vdx.fit
pddf	/app/data/pr_computation/vd/9vdx/9vdx.pr.out
profile	/app/data/saxs_computation/vd/9vdx/9vdx.dat

Serial synchrotron crystallography structure of a photosynthetic reaction center using a goniometer-compatible 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 (15)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 non-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 non-polymer

Entity 14 non-polymer

Entity 15 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)