36EZ | pdb_000036ez

Crystal structure of thiocyanate bound bovine cytochrome c oxidase

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	PEG4000, Potassium phosphate, Decylmaltoside

Crystal Properties
Matthews coefficient	Solvent content
4.19	70.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.316	α = 90
b = 185.058	β = 90
c = 208.477	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		2022-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	2.06641	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	2.388	138.398	95.6	0.138	0.998	14.7	13.1		178585

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	2.388	2.666			1.405	0.665

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.388	30.002	178421	8964	65.608	0.19	0.1869	0.1929	0.2418	0.2423	52.314

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]
0.353			-0.823		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.941
r_dihedral_angle_4_deg	18.762
r_dihedral_angle_3_deg	16.857
r_lrange_it	10.838
r_lrange_other	10.838
r_dihedral_angle_1_deg	7.04
r_scangle_it	6.723
r_scangle_other	6.723
r_dihedral_angle_other_3_deg	6.436
r_mcangle_it	5.697
r_mcangle_other	5.697
r_scbond_it	4.229
r_scbond_other	4.229
r_mcbond_it	3.711
r_mcbond_other	3.711
r_angle_refined_deg	1.672
r_angle_other_deg	1.318
r_nbd_refined	0.226
r_symmetry_nbd_refined	0.223
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.184
r_nbd_other	0.172
r_metal_ion_refined	0.167
r_xyhbond_nbd_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.156
r_chiral_restr	0.132
r_symmetry_xyhbond_nbd_other	0.087
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28488
Nucleic Acid Atoms
Solvent Atoms	589
Heterogen Atoms	2742

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
MOLREP	phasing