7TIE

Structure of oxidized bovine cytochrome c oxidase at 1.90 Angstrom resolution obtained by synchrotron X-rays

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
4.13	70.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.118	α = 90
b = 182.415	β = 90
c = 208.547	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		2019-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.9	40	99.9	0.139	0.996	7.8	6.9		528165

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2			2.105	0.442

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	1.9	39.989	528021	26755	99.833	0.186	0.1846	0.2152	43.502

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]
-2.807			-0.347		3.154

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.631
r_dihedral_angle_4_deg	16.843
r_dihedral_angle_3_deg	15.564
r_lrange_it	8.638
r_lrange_other	8.638
r_scangle_it	6.975
r_scangle_other	6.975
r_dihedral_angle_1_deg	6.631
r_mcangle_it	4.876
r_mcangle_other	4.876
r_scbond_it	4.843
r_scbond_other	4.843
r_mcbond_it	3.556
r_mcbond_other	3.556
r_dihedral_angle_other_3_deg	2.257
r_chiral_restr_other	2.066
r_angle_refined_deg	1.767
r_angle_other_deg	1.403
r_nbd_refined	0.216
r_symmetry_xyhbond_nbd_refined	0.198
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.179
r_nbd_other	0.176
r_symmetry_nbd_refined	0.175
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.088
r_symmetry_xyhbond_nbd_other	0.049
r_xyhbond_nbd_other	0.021
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.005
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28488
Nucleic Acid Atoms
Solvent Atoms	1693
Heterogen Atoms	2732

Software

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