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Crystal structure of HIV-1 Protease multiple mutants PRS17 bound to inhibitor Amprenavir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 37.5% Tacsimate (Hampton Research)
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.994 α = 90 b = 62.994 β = 90 c = 82.691 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2018-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.47 50 98.6 0.063 0.066 0.021 21.5 9.8 31170
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.52 95.7 1.124 1.198 0.406 0.664 8.2
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 5T2Z 1.47 32.97 29585 1569 98.64 0.2006 0.1993 0.2091 0.2272 0.2352 RANDOM 31.515
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] 0.39 0.19 0.39 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.99 r_dihedral_angle_4_deg 20.966 r_dihedral_angle_1_deg 15.005 r_dihedral_angle_3_deg 13.373 r_angle_refined_deg 2.396 r_angle_other_deg 1.439 r_chiral_restr 0.129 r_bond_refined_d 0.018 r_gen_planes_refined 0.015 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.99 r_dihedral_angle_4_deg 20.966 r_dihedral_angle_1_deg 15.005 r_dihedral_angle_3_deg 13.373 r_angle_refined_deg 2.396 r_angle_other_deg 1.439 r_chiral_restr 0.129 r_bond_refined_d 0.018 r_gen_planes_refined 0.015 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1522 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction