3IBD | pdb_00003ibd

Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q6N	ENSEMBLE OF PDB ID 2Q6N (A CHAIN), 1SUO, 2BDM, 3G5N (A CHAIN) EACH WITH RESIDUES 101-120, 205-232 OMITTED
experimental model	PDB	1SUO	ENSEMBLE OF PDB ID 2Q6N (A CHAIN), 1SUO, 2BDM, 3G5N (A CHAIN) EACH WITH RESIDUES 101-120, 205-232 OMITTED
experimental model	PDB	2BDM	ENSEMBLE OF PDB ID 2Q6N (A CHAIN), 1SUO, 2BDM, 3G5N (A CHAIN) EACH WITH RESIDUES 101-120, 205-232 OMITTED
experimental model	PDB	3G5N	ENSEMBLE OF PDB ID 2Q6N (A CHAIN), 1SUO, 2BDM, 3G5N (A CHAIN) EACH WITH RESIDUES 101-120, 205-232 OMITTED

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5	291	0.1 M sodium acetate (pH 5.5), 0.2 M potassium thiocyanate, 10% (w/v) PEG 1000, 10% (w/v) PEG 8000, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.573	α = 90
b = 55.74	β = 96.51
c = 99.09	γ = 90

Symmetry
Space Group	C 1 2 1

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		2009-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		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	1.998	98.451	98.3	0.131	0.131	11.8	6.9		32536

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)
1	2	2.11	88.1		0.487	0.487	1.4	4.1

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 (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	ENSEMBLE OF PDB ID 2Q6N (A CHAIN), 1SUO, 2BDM, 3G5N (A CHAIN) EACH WITH RESIDUES 101-120, 205-232 OMITTED	2	98.45	32545	32494	1640	98.1	0.181	0.178	0.18	0.228	0.23	RANDOM	21.92

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]
0.88		-0.26	-0.69		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.825
r_dihedral_angle_4_deg	19.742
r_dihedral_angle_3_deg	17.358
r_dihedral_angle_1_deg	6.384
r_scangle_it	4.813
r_scbond_it	3.03
r_mcangle_it	1.925
r_angle_refined_deg	1.767
r_mcbond_it	1.061
r_symmetry_vdw_refined	0.32
r_nbtor_refined	0.316
r_nbd_refined	0.232
r_symmetry_hbond_refined	0.198
r_xyhbond_nbd_refined	0.173
r_chiral_restr	0.122
r_metal_ion_refined	0.035
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
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	3699
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	89

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction