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Crystal structure of human cytochrome P450 3A4
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 7.5 0.1M HEPES PH 7.5, 0.025M NACL, 7.5% (V/V) ISOPROPANOL, 10
Crystal Properties Matthews coefficient Solvent content 2.4 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.94 α = 90 b = 100.91 β = 90 c = 131 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS 4 2003-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 2.74 40 94.7 0.04 10.8 2.8 13241
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 2.74 2.89 97.1 0.308 2.5 2.7
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 PDB ENTRY 1W0E 2.73 81.65 12577 689 93.9 0.238 0.234 0.3723 0.318 0.3559 RANDOM 78.73
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] -0.36 0.63 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.691 r_dihedral_angle_3_deg 20.273 r_dihedral_angle_4_deg 17.719 r_dihedral_angle_1_deg 9.32 r_scangle_it 4.382 r_mcangle_it 4.282 r_mcbond_it 3.392 r_scbond_it 3.315 r_angle_refined_deg 1.753 r_angle_other_deg 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.691 r_dihedral_angle_3_deg 20.273 r_dihedral_angle_4_deg 17.719 r_dihedral_angle_1_deg 9.32 r_scangle_it 4.382 r_mcangle_it 4.282 r_mcbond_it 3.392 r_scbond_it 3.315 r_angle_refined_deg 1.753 r_angle_other_deg 1.05 r_mcbond_other 0.913 r_nbd_refined 0.27 r_nbd_other 0.205 r_nbtor_refined 0.204 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.178 r_symmetry_vdw_other 0.171 r_chiral_restr 0.123 r_xyhbond_nbd_other 0.123 r_nbtor_other 0.092 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 3652 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling