7TII

Annealed 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	2DYR

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
4.07	69.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.037	α = 90
b = 182.633	β = 90
c = 205.453	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	0.9790	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	2.45	40	99.85	0.993	6.9	6.9		244470

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	2.45	2.49	99.9		0.402	0.9

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	2DYR	2.45	39.303	244470	12054	99.851	0.209	0.2063	0.253	46.829

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]
-3.551			-1.654		5.205

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.253
r_dihedral_angle_3_deg	17.352
r_dihedral_angle_4_deg	16.426
r_lrange_it	8.711
r_lrange_other	8.711
r_dihedral_angle_1_deg	6.977
r_scangle_it	6.296
r_scangle_other	6.296
r_mcangle_it	5.165
r_mcangle_other	5.165
r_dihedral_angle_other_3_deg	4.395
r_scbond_it	3.95
r_scbond_other	3.95
r_mcbond_it	3.303
r_mcbond_other	3.303
r_chiral_restr_other	2.047
r_angle_refined_deg	1.622
r_angle_other_deg	1.262
r_symmetry_nbd_refined	0.228
r_nbd_refined	0.215
r_nbd_other	0.212
r_symmetry_xyhbond_nbd_refined	0.195
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.162
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_other	0.038
r_bond_refined_d	0.008
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	914
Heterogen Atoms	2276

Software

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