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Crystal Structure of human Cytochrome P450 2B6 (Y226H/K262R) in complex with an analog of a drug Efavirenz
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 0.8M Sodium Formate
0.1 M Tris pH 7.5
8% w/v PEG 20000
8% v/v PEG 550 MME
Crystal Properties Matthews coefficient Solvent content 3.77 67.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.293 α = 90 b = 197.786 β = 98.51 c = 119.222 γ = 90
Symmetry Space Group P 1 21 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 2017-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.99 50 98.9 0.188 6.4 3.3 89926
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 2.99 3.07 96.7 0.1 1.6 3.2
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 2.99 50 89926 4745 99.2 0.229 0.227 0.2363 0.262 0.2673 RANDOM 49.63
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] -2.57 3.2 -2.59 6.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.232 r_dihedral_angle_4_deg 20.536 r_dihedral_angle_3_deg 20.02 r_dihedral_angle_1_deg 6.459 r_angle_refined_deg 1.659 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.232 r_dihedral_angle_4_deg 20.536 r_dihedral_angle_3_deg 20.02 r_dihedral_angle_1_deg 6.459 r_angle_refined_deg 1.659 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 21849 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 566
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing