5VJS | pdb_00005vjs

De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, a synthetic Zn porphyrin, and Zn(II) cations

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.4	277	3.4 M NaCl, 100 mM Na acetate

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.749	α = 90
b = 43.749	β = 90
c = 245.737	γ = 90

Symmetry
Space Group	P 41 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	100	CCD	ADSC QUANTUM 270	Oxford Danfysik toroidal focusing mirror	2013-11-20	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	1.0781, 1.2824, 1.2831	NSLS	X6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	61.43	99.4	0.085	0.091	0.999	16.8	7.603		17105		-3	37.05

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	98.8		0.97	1.041	0.888	2.52	7.409

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2	61.43	16280	830	99.33	0.2366	0.2345	0.24	0.2779	0.28	RANDOM	40.772

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]
2.38			2.38		-4.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.585
r_dihedral_angle_4_deg	16.471
r_dihedral_angle_3_deg	16.185
r_dihedral_angle_1_deg	4.947
r_angle_refined_deg	1.829
r_angle_other_deg	1.095
r_chiral_restr	0.114
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_gen_planes_other	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.585
r_dihedral_angle_4_deg	16.471
r_dihedral_angle_3_deg	16.185
r_dihedral_angle_1_deg	4.947
r_angle_refined_deg	1.829
r_angle_other_deg	1.095
r_chiral_restr	0.114
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_gen_planes_other	0.009
r_bond_other_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1585
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
AutoSol	phasing
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.