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Crystal structure of P450 2B4(H226Y) in complex with paroxetine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MVR PDB ENTRY 3MVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.1 M HEPES, 2M Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.37 63.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.76 α = 90 b = 90.76 β = 90 c = 153.681 γ = 120
Symmetry Space Group P 31 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 2010-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.98 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 2.137 78.6 99.6 0.064 0.064 8.2 11.1 41220 41055
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 2.137 2.25 99.4 0.444 0.444 1.7 11.1
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 (All) 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 PDB ENTRY 3MVR 2.14 78.6 39214 38955 2066 99.3 0.19 0.19 0.187 0.2088 0.229 0.2362 RANDOM 40.305
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] 0.03 0.01 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.506 r_dihedral_angle_4_deg 18.405 r_dihedral_angle_3_deg 14.915 r_dihedral_angle_1_deg 6.439 r_scangle_it 4.67 r_scbond_it 3.037 r_mcangle_it 1.987 r_angle_refined_deg 1.904 r_mcbond_it 1.102 r_chiral_restr 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.506 r_dihedral_angle_4_deg 18.405 r_dihedral_angle_3_deg 14.915 r_dihedral_angle_1_deg 6.439 r_scangle_it 4.67 r_scbond_it 3.037 r_mcangle_it 1.987 r_angle_refined_deg 1.904 r_mcbond_it 1.102 r_chiral_restr 0.13 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 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 3654 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 183
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection iMOSFLM data reduction SCALA data scaling PHASER phasing