6J8M | pdb_00006j8m

Low-dose structure of bovine heart cytochrome c oxidase in the fully oxidized state determined using 30 keV X-ray

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5B1B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	5.8	277	PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
4.01	69.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 182.02	α = 90
b = 203.54	β = 90
c = 177.41	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS3 X CdTe 300K	Undulator 3rd harmonic, Compound refractive lends	2016-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.4133	SPring-8	BL41XU

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	1.9	40	98.09	0.099	0.11	0.047	0.994	8.1	4.9		503312			38.511

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	1.9	1.97	96.33		0.973	1.116	0.535	0.697	1.4	4.23

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	5B1B	1.9	40	478268	25030	98.03	0.1735	0.1721	0.17	0.1992	0.23	RANDOM	42.87

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]
0.42			0.86		-1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.226
r_dihedral_angle_4_deg	17.139
r_dihedral_angle_3_deg	15.01
r_dihedral_angle_1_deg	5.921
r_sphericity_bonded	5.461
r_rigid_bond_restr	4.571
r_angle_refined_deg	1.659
r_chiral_restr	0.109
r_bond_refined_d	0.014
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28506
Nucleic Acid Atoms
Solvent Atoms	2558
Heterogen Atoms	2234

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	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.