1NTK | pdb_00001ntk

Crystal Structure of Mitochondrial Cytochrome bc1 in Complex with Antimycin A1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.2	277	PEG 4000, ammonium acetate, potassium chloride, glycerol, DMG/SPC, MOPS, pH 7.2, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.66	66.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.785	α = 90
b = 153.785	β = 90
c = 592.498	γ = 90

Symmetry
Space Group	I 41 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	CCD	ADSC QUANTUM 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9B	1.0	NSLS	X9B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.6	50	98.5			109171	107555	-1	-1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.667	95.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2.6	40	107555	104312	3224	98.52	0.23421	0.23421	0.23307	0.27049	RANDOM	35.172

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]
1.24			1.24		-2.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.815
r_scangle_it	4.847
r_dihedral_angle_1_deg	3.547
r_scbond_it	2.977
r_angle_refined_deg	1.802
r_mcangle_it	1.769
r_mcbond_it	0.95
r_chiral_restr	0.26
r_nbd_refined	0.256
r_symmetry_hbond_refined	0.241

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.815
r_scangle_it	4.847
r_dihedral_angle_1_deg	3.547
r_scbond_it	2.977
r_angle_refined_deg	1.802
r_mcangle_it	1.769
r_mcbond_it	0.95
r_chiral_restr	0.26
r_nbd_refined	0.256
r_symmetry_hbond_refined	0.241
r_symmetry_vdw_refined	0.237
r_xyhbond_nbd_refined	0.193
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16605
Nucleic Acid Atoms
Solvent Atoms	342
Heterogen Atoms	171

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

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.