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Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole
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 0.181 0.228 0.2336 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
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