7ZVZ

Cytochrome c prime beta from Methylococcus capsulatus (Bath): Chemically Reduced Ferrous Form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6HIH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	15 mg/ml protein mixed with 10 mM ZnSO4, 35% PEG 550, 100 mM MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.56	α = 90
b = 105.56	β = 90
c = 105.56	γ = 90

Symmetry
Space Group	P 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2016-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.68	43.09	100	0.044	0.048	0.018	1	24.2	6.7		44860

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.68	1.72	100		1.315	1.424	0.541	0.551		6.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6HIH	1.68	37.35	42598	2216	99.95	0.1937	0.1921	0.2283	RANDOM	31.401

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.195
r_dihedral_angle_4_deg	20.063
r_dihedral_angle_3_deg	12.389
r_dihedral_angle_1_deg	6.894
r_angle_refined_deg	2.322
r_angle_other_deg	1.417
r_chiral_restr	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.014
r_gen_planes_other	0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.195
r_dihedral_angle_4_deg	20.063
r_dihedral_angle_3_deg	12.389
r_dihedral_angle_1_deg	6.894
r_angle_refined_deg	2.322
r_angle_other_deg	1.417
r_chiral_restr	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.014
r_gen_planes_other	0.014
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2144
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	105

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
REFMAC	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.