3ME6 | pdb_00003me6

Crystal structure of cytochrome 2B4 in complex with the anti-platelet drug clopidogrel

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	291	20% (w/v) PEG 8000, 0.2 M NaCl and 0.1 M phosphate-citrate, pH 4.2, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
4.2	70.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 234.49	α = 90
b = 234.49	β = 90
c = 57.32	γ = 120

Symmetry
Space Group	P 3

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	MARMOSAIC 325 mm CCD		2009-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.98	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3.1	76.755	97.7	0.13	0.13	4.7	4	62529	62529

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.1	3.18	98.6		0.432	0.432	3.5	3.9	9259

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1SUO	3.1	76.75	62529	62516	3169	97.67	0.181	0.181	0.178	0.18	0.234	0.23	RANDOM	42.197

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]
-0.06	-0.03		-0.06		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.623
r_dihedral_angle_4_deg	21.325
r_dihedral_angle_3_deg	19.993
r_dihedral_angle_1_deg	7.116
r_scangle_it	4.267
r_scbond_it	2.404
r_angle_refined_deg	1.936
r_mcangle_it	1.715
r_mcbond_it	0.864
r_chiral_restr	0.132

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.623
r_dihedral_angle_4_deg	21.325
r_dihedral_angle_3_deg	19.993
r_dihedral_angle_1_deg	7.116
r_scangle_it	4.267
r_scbond_it	2.404
r_angle_refined_deg	1.936
r_mcangle_it	1.715
r_mcbond_it	0.864
r_chiral_restr	0.132
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14882
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	256

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction

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.