7THU

Structure of reduced bovine cytochrome c oxidase at 1.93 Angstrom resolution obtained by synchrotron X-rays

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
4.13	70.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.182	α = 90
b = 182.282	β = 90
c = 208.683	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		2019-10-17	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)	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	1.93	40.003	99.2	0.999	12.6	6.8		500705

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	1.93	2.03			0.416	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	2DYR	1.93	40.003	500554	24681	99.129	0.185	0.1836	0.2125	46.817

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]
-2.323			-0.727		3.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.506
r_dihedral_angle_4_deg	16.537
r_dihedral_angle_other_3_deg	16.375
r_dihedral_angle_3_deg	16.33
r_lrange_other	9.075
r_lrange_it	9.072
r_scangle_it	7.166
r_scangle_other	7.165
r_dihedral_angle_1_deg	6.422
r_mcangle_it	4.968
r_mcangle_other	4.968
r_scbond_it	4.965
r_scbond_other	4.965
r_mcbond_it	3.641
r_mcbond_other	3.641
r_chiral_restr_other	2.042
r_angle_refined_deg	1.809
r_angle_other_deg	1.424
r_nbd_other	0.225
r_nbd_refined	0.214
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_other	0.177
r_symmetry_nbd_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.158
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.143
r_symmetry_nbtor_other	0.092
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28584
Nucleic Acid Atoms
Solvent Atoms	1381
Heterogen Atoms	2730

Software

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