7TIH

Structure of oxidized bovine cytochrome c oxidase with reduced metal centers induced by synchrotron X-ray exposure

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7TIE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6.8	277	PEG 4000, Potassium phosphate, Decylmaltoside

Crystal Properties
Matthews coefficient	Solvent content
4.08	69.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.037	α = 90
b = 182.696	β = 90
c = 205.854	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 PILATUS 6M		2019-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9795	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.35	39.339	99.9	0.993	6.7	6.9		277487

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.48			0.456	1

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7TIE	2.35	39.339	277374	13603	99.852	0.195	0.193	0.2351	45.597

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]
-3.727			-1.208		4.935

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.334
r_dihedral_angle_3_deg	16.705
r_dihedral_angle_4_deg	14.652
r_lrange_other	8.548
r_lrange_it	8.546
r_dihedral_angle_other_3_deg	7.212
r_dihedral_angle_1_deg	6.837
r_scangle_it	6.346
r_scangle_other	6.346
r_mcangle_it	4.896
r_mcangle_other	4.896
r_scbond_it	4.014
r_scbond_other	4.014
r_mcbond_it	3.153
r_mcbond_other	3.153
r_chiral_restr_other	2.048
r_angle_refined_deg	1.618
r_angle_other_deg	1.287
r_nbd_refined	0.211
r_nbd_other	0.182
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.162
r_symmetry_nbd_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.152
r_metal_ion_refined	0.141
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.068
r_symmetry_xyhbond_nbd_other	0.032
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28488
Nucleic Acid Atoms
Solvent Atoms	1529
Heterogen Atoms	2704

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing