3FYE | pdb_00003fye

Catalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides in the reduced state

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GSM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	277	23-24% PEG-400, crystal reduced by dithionite, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.9	68.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.613	α = 90
b = 131.472	β = 90
c = 176.192	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 300 mm CCD		2007-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0332	APS	23-ID-B

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	2.12	50	98.5	0.066		4.6		162159

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)
	2.15	2.206	92.7		0.606		4	10331

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2GSM	2.15	50	151414	151414	4375	99.09	0.196	0.196	0.196	0.1968	0.221	0.2207	RANDOM	45.8

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]
-2.03			-0.22		2.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.07
r_dihedral_angle_4_deg	18.729
r_dihedral_angle_3_deg	13.707
r_dihedral_angle_1_deg	5.667
r_scangle_it	2.042
r_scbond_it	1.432
r_angle_refined_deg	1.227
r_mcangle_it	1.025
r_mcbond_it	0.625
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.07
r_dihedral_angle_4_deg	18.729
r_dihedral_angle_3_deg	13.707
r_dihedral_angle_1_deg	5.667
r_scangle_it	2.042
r_scbond_it	1.432
r_angle_refined_deg	1.227
r_mcangle_it	1.025
r_mcbond_it	0.625
r_nbtor_refined	0.31
r_symmetry_hbond_refined	0.207
r_symmetry_vdw_refined	0.203
r_nbd_refined	0.196
r_metal_ion_refined	0.127
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12452
Nucleic Acid Atoms
Solvent Atoms	480
Heterogen Atoms	679

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	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.