6JY3

Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5B1A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		277	sodium phosphate, PEG 4000, DM

Crystal Properties
Matthews coefficient	Solvent content
4.84	74.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.529	α = 90
b = 152.131	β = 90
c = 174.083	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	50	CCD	RAYONIX MX225HE		2011-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim 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	1.8	200	99.3	0.031	29.3	7.4		361138

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.82			0.459	0.765	2

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	5B1A	1.85	40	316483	16494	99.04	0.15326	0.15125	0.17	0.19162	0.2	RANDOM	43.877

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]
0.86			3.49		-4.35

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	48.503
r_dihedral_angle_2_deg	34.292
r_sphericity_bonded	25.134
r_dihedral_angle_4_deg	15.806
r_dihedral_angle_3_deg	14.15
r_scangle_other	10.151
r_scbond_it	9.66
r_scbond_other	9.66
r_long_range_B_refined	9.148
r_long_range_B_other	9.09
r_mcangle_it	7.233
r_mcangle_other	7.233
r_rigid_bond_restr	6.906
r_mcbond_it	6.665
r_mcbond_other	6.655
r_dihedral_angle_1_deg	5.877
r_angle_refined_deg	2.039
r_angle_other_deg	1.002
r_chiral_restr	0.119
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
r_gen_planes_other	0.005
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13851
Nucleic Acid Atoms
Solvent Atoms	662
Heterogen Atoms	729

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing