3HB3

High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	277	25% glycerol, pH 5.5, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.02	69.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.403	α = 90
b = 150.473	β = 90
c = 157.185	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	CCD	MARMOSAIC 225 mm CCD		2005-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9198	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.25	111.8	99.04	0.124	14.2	4.9	90709	90709	-3	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.25	2.32	98.3		0.379	3.2	4.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1AR1	2.25	19.98	-3	90709	90709	2819	99.04	0.22024	0.22024	0.21836	0.27996	RANDOM	45.272

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_1_deg	8.795
r_scangle_it	5.166
r_scbond_it	3.538
r_angle_refined_deg	2.683
r_mcangle_it	2.407
r_mcbond_it	1.381
r_symmetry_vdw_refined	0.323
r_symmetry_hbond_refined	0.313
r_nbd_refined	0.264
r_xyhbond_nbd_refined	0.234

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.795
r_scangle_it	5.166
r_scbond_it	3.538
r_angle_refined_deg	2.683
r_mcangle_it	2.407
r_mcbond_it	1.381
r_symmetry_vdw_refined	0.323
r_symmetry_hbond_refined	0.313
r_nbd_refined	0.264
r_xyhbond_nbd_refined	0.234
r_chiral_restr	0.23
r_bond_refined_d	0.031
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7956
Nucleic Acid Atoms
Solvent Atoms	554
Heterogen Atoms	883

Software

Software
Software Name	Purpose
MAR345dtb	data collection
EPMR	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.