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Crystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in complex with the inhibitor 4-(4-Nitrobenzyl)pyridine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IBD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 291 0.15 M DL-Malic Acid, 20 % w/v PEG 3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.74 55.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.88 α = 90 b = 101.88 β = 90 c = 299.509 γ = 120
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 2010-12-11 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 2.8 84.6 88.9 0.063 0.063 9.6 2.6 76085 52.67
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 2.8 2.95 78.6 0.368 0.368 2.1 2.4
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 3IBD 2.8 50.51 81196 72191 3815 88.9 0.22 0.218 0.2264 0.259 0.2643 RANDOM 52.67
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] 0.74 0.37 0.74 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.135 r_dihedral_angle_4_deg 20.867 r_dihedral_angle_3_deg 18.436 r_dihedral_angle_1_deg 6.345 r_scangle_it 3.337 r_scbond_it 1.884 r_angle_refined_deg 1.719 r_mcangle_it 1.24 r_mcbond_it 0.613 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.135 r_dihedral_angle_4_deg 20.867 r_dihedral_angle_3_deg 18.436 r_dihedral_angle_1_deg 6.345 r_scangle_it 3.337 r_scbond_it 1.884 r_angle_refined_deg 1.719 r_mcangle_it 1.24 r_mcbond_it 0.613 r_chiral_restr 0.122 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 22228 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 586
Software Software Software Name Purpose Blu-Ice data collection BALBES phasing REFMAC refinement iMOSFLM data reduction SCALA data scaling