2FYU | pdb_00002fyu

Crystal structure of bovine heart mitochondrial bc1 with jg144 inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L0N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	277.2	50 mM MOPS 7.2pH, 20 mM Ammonium acetate, 20% glycerol.Incubation with 2-5 mol excess of JG144. Precipitant 12% PEG4000, 0.5 M KCl, 0.1% DHPC; Protein:PPT ratio 1:0.57, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K

Crystal Properties
Matthews coefficient	Solvent content
3.64	66.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.263	α = 90
b = 154.263	β = 90
c = 590.191	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	AREA DETECTOR	MARRESEARCH		2004-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0090	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	2.26	50	86.1	0.056	17.2	4		157290		-0.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.26	2.34	42.4		0.382		1.8	13582

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	1l0n	2.26	40	157290	157290	3230	96.89	0.24916	0.24916	0.24843	0.28328	RANDOM	25.239

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]
2.36			2.36		-4.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	11.115
r_scangle_it	7.314
r_scbond_it	5.686
r_mcangle_it	2.514
r_angle_refined_deg	2.063
r_mcbond_it	0.592
r_chiral_restr	0.2
r_nbd_refined	0.117
r_xyhbond_nbd_refined	0.096
r_symmetry_vdw_refined	0.094
r_symmetry_hbond_refined	0.068
r_gen_planes_refined	0.026
r_bond_refined_d	0.021
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16477
Nucleic Acid Atoms
Solvent Atoms	267
Heterogen Atoms	156

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling