4W9Z | pdb_00004w9z

Crystal structure of the periplasmic domain of subunit II of cytochrome oxidase (CoxB) of Bradyrhizobium japonicum

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4TXV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.2M Potassium bromide, 0.1M Tris pH 7.5, 10% PEG1000, 10% PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.431	α = 90
b = 38.612	β = 97.63
c = 59.644	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	80	PIXEL	DECTRIS PILATUS 6M		2014-08-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.3		99.2	0.048	0.053	20.13			35883		-3	16.269

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.33	99.5		0.247	0.272	5.25

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	4TXV	1.3	59.12	34089	1795	99.2	0.1102	0.1089	0.11	0.1336	0.13	RANDOM	16.637

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]
-0.28		-0.08	0.46		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	37.673
r_dihedral_angle_2_deg	35.294
r_sphericity_bonded	15.054
r_dihedral_angle_4_deg	14.59
r_dihedral_angle_3_deg	13.508
r_dihedral_angle_1_deg	8.812
r_rigid_bond_restr	6.327
r_mcangle_it	3.219
r_mcbond_it	2.457
r_mcbond_other	2.409

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	37.673
r_dihedral_angle_2_deg	35.294
r_sphericity_bonded	15.054
r_dihedral_angle_4_deg	14.59
r_dihedral_angle_3_deg	13.508
r_dihedral_angle_1_deg	8.812
r_rigid_bond_restr	6.327
r_mcangle_it	3.219
r_mcbond_it	2.457
r_mcbond_other	2.409
r_angle_refined_deg	2.27
r_angle_other_deg	1.238
r_chiral_restr	0.131
r_bond_refined_d	0.026
r_gen_planes_refined	0.01
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1091
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Coot	model building
PDB_EXTRACT	data extraction
XSCALE	data scaling
PHASER	phasing
XSCALE	data reduction

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.