7ZQZ | pdb_00007zqz

F61V Cytochrome c prime beta from Methylococcus capsulatus (Bath): NO complex

X-RAY DIFFRACTION

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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	2 microlitres of 15 mg/ml protein in 0.1 M HEPES buffer, pH 7.5, mixed with with an equivalent volume of reservoir solution containing 0.01 M ZnSO4, 35% PEG 550 (v/v) and 0.1 M MES, pH 6.5. Cryoprotection in ML plus 10% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.236	α = 90
b = 106.236	β = 90
c = 106.236	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 EIGER2 XE 16M		2019-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	33.59	99.3	0.042	0.05	0.028	0.999	11.7	3		45336

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	99.5		0.758	0.919	0.511	0.579		2.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6HIH	1.68	33.59	42969	2318	99.1	0.1792	0.1779	0.1868	0.2019	0.1911	RANDOM	31.457

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	32.4
r_dihedral_angle_4_deg	20.816
r_dihedral_angle_3_deg	12.339
r_dihedral_angle_1_deg	7.16
r_angle_refined_deg	1.859
r_angle_other_deg	1.486
r_chiral_restr	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.014
r_gen_planes_other	0.014
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2099
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	117

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
REFMAC	phasing