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Crystal structure of CYP3A4 ligated to oxazole-substituted desoxyritonavir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NXU PDB ENTRY 3NXU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 6 298 PEG 3350, sodium malonate, pH 6.0, microbatch under oil, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 43.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.655 α = 90 b = 99.585 β = 90 c = 126.375 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 200 CCD ADSC QUANTUM 315 mirrors 2012-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.127 SSRL BL7-1
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 2.718 49.8 99.9 0.072 18.9 9.4 12248 12236 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 2.718 2.79 98.9 0.505 3.5 5.4 845
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 3NXU 2.718 49.79 2 12733 12710 661 99.82 0.20661 0.2034 0.2022 0.26971 0.2687 RANDOM 91.946
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 -0.04 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.74 r_dihedral_angle_4_deg 23.294 r_dihedral_angle_3_deg 20.592 r_dihedral_angle_1_deg 6.281 r_angle_refined_deg 1.894 r_chiral_restr 0.092 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.74 r_dihedral_angle_4_deg 23.294 r_dihedral_angle_3_deg 20.592 r_dihedral_angle_1_deg 6.281 r_angle_refined_deg 1.894 r_chiral_restr 0.092 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3695 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 92
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling