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Crystal Structure of the complex between human cytochrome P450 3A4 and desthiazolylmethyloxycarbonyl ritonavir
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 6.4 293 10% PEG3350, 80 mM malonate, pH 6.4, MICROBATCH UNDER OIL, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.79 α = 90 b = 98.6 β = 90 c = 125.07 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 83 CCD ADSC QUANTUM 315r 2010-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.0 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 2.25 49.3 98.8 0.074 11 6.5 23463 23181 39.7
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 2.25 2.37 99.7 0.434 3.2 6.3 3360
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 (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 2.25 38.4 22309 21981 1177 98.53 0.2314 0.22799 0.2278 0.29735 0.2964 RANDOM 57.724
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] 4 -1.49 -2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.98 r_dihedral_angle_4_deg 24.317 r_dihedral_angle_3_deg 20.261 r_dihedral_angle_1_deg 7.371 r_scangle_it 4.277 r_scbond_it 2.769 r_angle_refined_deg 1.955 r_mcangle_it 1.698 r_mcbond_it 0.941 r_chiral_restr 0.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.98 r_dihedral_angle_4_deg 24.317 r_dihedral_angle_3_deg 20.261 r_dihedral_angle_1_deg 7.371 r_scangle_it 4.277 r_scbond_it 2.769 r_angle_refined_deg 1.955 r_mcangle_it 1.698 r_mcbond_it 0.941 r_chiral_restr 0.137 r_bond_refined_d 0.02 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3609 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 84
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling