5VJU | pdb_00005vju

De Novo Photosynthetic Reaction Center Protein Variant Equipped with His-Tyr H-bond, Heme B, and Cd(II) ions

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	277	24% w/v PEG 1500, 70 mM CdCl2, 100 mM Na acetate

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.485	α = 90
b = 25.876	β = 103.64
c = 73.708	γ = 90

Symmetry
Space Group	P 1 21 1

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	RIGAKU SATURN 944+	Osmic VariMax mirror	2015-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54178

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	2.02	71.63	97.3	0.051	0.055	0.999	25.98	6.705		10744		-3	25.547

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	2.02	2.07	71		0.101	0.12	0.983	9.46	3.347

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.08	71.63	9587	527	98.64	0.1869	0.1834	0.19	0.2434	0.25	RANDOM	31.833

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]
0.53		-0.27	0.94		-1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.432
r_dihedral_angle_4_deg	17.954
r_dihedral_angle_3_deg	15.39
r_dihedral_angle_1_deg	6.322
r_angle_refined_deg	1.782
r_angle_other_deg	1.027
r_chiral_restr	0.104
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_gen_planes_other	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.432
r_dihedral_angle_4_deg	17.954
r_dihedral_angle_3_deg	15.39
r_dihedral_angle_1_deg	6.322
r_angle_refined_deg	1.782
r_angle_other_deg	1.027
r_chiral_restr	0.104
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1587
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	49

Software

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

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.