9VDX | pdb_00009vdx

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

X-RAY DIFFRACTION

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Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NJ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	400 microliter heptane-triol, 20 microliter 1M Potassium Phosphate pH 6.8, 475mg Ammonium Sulphate

Crystal Properties
Matthews coefficient	Solvent content
5.37	77.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 223.8	α = 90
b = 223.8	β = 90
c = 113.5	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS EIGER X 16M		2021-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.98	MAX IV	BioMAX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		fixed target

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.8	37	100	0.936	4.1	412		151216

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9			0.529

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.8	36.8	70965	3534	99.629	0.21	0.215	0.2152	0.253	0.2539	50.965

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.505			0.505		-1.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.989
r_dihedral_angle_6_deg	15.113
r_lrange_other	11.424
r_lrange_it	11.421
r_dihedral_angle_2_deg	7.699
r_scangle_it	7.308
r_scangle_other	7.308
r_dihedral_angle_1_deg	7.302
r_mcangle_it	6.635
r_mcangle_other	6.634
r_scbond_it	4.677
r_scbond_other	4.677
r_mcbond_it	4.33
r_mcbond_other	4.329
r_angle_refined_deg	2.191
r_angle_other_deg	0.583
r_nbd_refined	0.249
r_symmetry_nbd_refined	0.246
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.193
r_xyhbond_nbd_refined	0.168
r_nbd_other	0.118
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.071
r_symmetry_xyhbond_nbd_other	0.061
r_symmetry_xyhbond_nbd_refined	0.048
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9346
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	909

Software

Software
Software Name	Purpose
MxCuBE	data collection
CrystFEL	data reduction
PHASER	phasing
REFMAC	refinement
Coot	model building