6JY4

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

X-RAY DIFFRACTION

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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		277	sodium phosphate, PEG 4000, DM

Crystal Properties
Matthews coefficient	Solvent content
5.04	75.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.395	α = 90
b = 152.395	β = 90
c = 174.04	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	1.9	200	89.5	0.032	28.2	9		278336

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	1.9	1.92			0.373	0.734	2.2

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	5B1B	1.95	40	243663	12837	89.16	0.15492	0.15228	0.17	0.20454	0.21	RANDOM	47.214

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]
2.15			2.84		-4.98

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	52.753
r_dihedral_angle_2_deg	33.803
r_sphericity_bonded	28.109
r_dihedral_angle_4_deg	17.135
r_dihedral_angle_3_deg	14.544
r_scangle_other	10.749
r_long_range_B_refined	9.774
r_long_range_B_other	9.743
r_scbond_it	9.739
r_scbond_other	9.738
r_mcangle_it	7.944
r_mcangle_other	7.944
r_mcbond_it	7.17
r_mcbond_other	7.169
r_rigid_bond_restr	6.386
r_dihedral_angle_1_deg	5.979
r_angle_refined_deg	1.938
r_angle_other_deg	0.947
r_chiral_restr	0.108
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
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	608
Heterogen Atoms	712

Software

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