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Crystal structure of human P450 3A4 in complex with ketoconazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W0E PDB ENTRY 1W0E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 HANGING DROP CRYSTALLISATION USING 1:1 RATIO OF PROTEIN AT 20-27 MG/ML IN A SOLUTION CONTAINING 50 MM POTASSIUM PHOSPHATE PH 7.2, 0.2 MM POTASSIUM CHLORIDE, 20% (V/V) GLYCEROL, 2 MM DITHIOTHREITOL, 1MM EDTA
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 228.942 α = 90 b = 66.363 β = 102.8 c = 146.419 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 ADSC CCD 2005-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.8 29.8 98.8 0.1 7.6 3.7 52714 2
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 2.8 2.87 98.1 0.38 5.5 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1W0E 2.8 30 2 49153 2654 97.1 0.22 0.218 0.2101 0.271 0.2614 31.89
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] 0.82 2.01 0.28 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.985 r_dihedral_angle_3_deg 18.854 r_dihedral_angle_4_deg 16.917 r_dihedral_angle_1_deg 5.217 r_scangle_it 1.205 r_angle_refined_deg 1.175 r_scbond_it 0.731 r_mcangle_it 0.715 r_mcbond_it 0.402 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.985 r_dihedral_angle_3_deg 18.854 r_dihedral_angle_4_deg 16.917 r_dihedral_angle_1_deg 5.217 r_scangle_it 1.205 r_angle_refined_deg 1.175 r_scbond_it 0.731 r_mcangle_it 0.715 r_mcbond_it 0.402 r_nbtor_refined 0.31 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.147 r_xyhbond_nbd_refined 0.145 r_bond_refined_d 0.08 r_chiral_restr 0.079 r_symmetry_hbond_refined 0.043 r_gen_planes_refined 0.003 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_refined 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_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 14650 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 418
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing