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Crystal structure of CYP2B6 (Y226H/K262R) in complex with a monoterpene bornane
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I91
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 291 0.2 M Sodium Chloride
0.1 M HEPES
25% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 3.24 62.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.49 α = 90 b = 77.49 β = 90 c = 202.15 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 Marm 2016-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
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 1.93 40.43 96.2 0.049 9.7 3.1 98894
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 1.93 2.03 97.7 0.229 3.2 3.1 14692
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4I91 1.93 40.43 94042 4852 96.19 0.17522 0.17337 0.1802 0.20993 0.2146 RANDOM 26.458
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] 0.64 0.32 0.64 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.032 r_dihedral_angle_4_deg 20.16 r_dihedral_angle_3_deg 14.659 r_dihedral_angle_1_deg 6.071 r_scangle_it 5.703 r_scbond_it 3.719 r_mcangle_it 2.455 r_angle_refined_deg 2.199 r_mcbond_it 1.424 r_chiral_restr 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.032 r_dihedral_angle_4_deg 20.16 r_dihedral_angle_3_deg 14.659 r_dihedral_angle_1_deg 6.071 r_scangle_it 5.703 r_scbond_it 3.719 r_mcangle_it 2.455 r_angle_refined_deg 2.199 r_mcbond_it 1.424 r_chiral_restr 0.17 r_bond_refined_d 0.03 r_gen_planes_refined 0.012 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7416 Nucleic Acid Atoms Solvent Atoms 481 Heterogen Atoms 222
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing iMOSFLM data reduction SCALA data scaling