9GCX | pdb_00009gcx

Crystal structure of bovine Cytochrome bc1 in complex with inhibitor F8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7R3V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	277	50 mM KPi pH 6.8, 100 mM NaCl, 3 mM NaN3, 10-20% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
4.83	74.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 210.082	α = 90
b = 210.082	β = 90
c = 344.844	γ = 120

Symmetry
Space Group	P 65 2 2

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 EIGER X 16M		2020-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97856	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	3.52	49.65	99.6	0.15	0.05	0.99	13.5	10.3		55657

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.54	3.62	96.5		0.51	0.54	1.6

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	3.522	30	55657	2830	99.106	0.19	0.1877	0.1878	0.2407	0.2407	124.215

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]
-0.316	-0.158		-0.316		1.026

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	19.372
r_dihedral_angle_3_deg	16.96
r_dihedral_angle_2_deg	16.924
r_scangle_it	15.641
r_dihedral_angle_6_deg	14.327
r_mcangle_it	11.98
r_scbond_it	10.54
r_mcbond_it	7.758
r_dihedral_angle_1_deg	7.5
r_angle_refined_deg	2.081

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	19.372
r_dihedral_angle_3_deg	16.96
r_dihedral_angle_2_deg	16.924
r_scangle_it	15.641
r_dihedral_angle_6_deg	14.327
r_mcangle_it	11.98
r_scbond_it	10.54
r_mcbond_it	7.758
r_dihedral_angle_1_deg	7.5
r_angle_refined_deg	2.081
r_symmetry_xyhbond_nbd_refined	0.383
r_nbtor_refined	0.318
r_nbd_refined	0.237
r_symmetry_nbd_refined	0.235
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.133
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15866
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	813

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.