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Crystal Structure of HIV-1 I50V, A71V Protease in Complex with the Protease Inhibitor Darunavir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TSU PDB entry 1TSU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 295 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 18-33% Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.16 42.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.62 α = 90 b = 63.344 β = 97.33 c = 58.648 γ = 90
Symmetry Space Group P 1 21 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 QUANTUM 315 Bent conical Si-mirror (Rh coated), Bent Ge(111) monochromator SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
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 1.95 50 99.6 0.088 8.4 4.4 26676
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 1.95 2.02 99.5 0.37 4.5
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 1TSU 1.95 31.67 25320 1339 99.25 0.17536 0.17303 0.1831 0.21841 0.2278 RANDOM 29.073
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] -2.18 -0.23 0.89 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.734 r_dihedral_angle_4_deg 18.453 r_dihedral_angle_3_deg 13.559 r_dihedral_angle_1_deg 7.48 r_scangle_it 4.963 r_scbond_it 3.106 r_mcangle_it 2.282 r_angle_other_deg 1.742 r_angle_refined_deg 1.37 r_mcbond_it 1.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.734 r_dihedral_angle_4_deg 18.453 r_dihedral_angle_3_deg 13.559 r_dihedral_angle_1_deg 7.48 r_scangle_it 4.963 r_scbond_it 3.106 r_mcangle_it 2.282 r_angle_other_deg 1.742 r_angle_refined_deg 1.37 r_mcbond_it 1.331 r_mcbond_other 0.204 r_chiral_restr 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2978 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 151
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling