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Atomic-resolution crystal structure of chemically-synthesized HIV-1 protease in complex with JG-365
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7HVP PDB ENTRY 7HVP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP well solution 0.1 M citrate, 0.2 M sodium phosphate, 30% saturated ammonium sulfate, and 10% DMSO, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.03 39.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.501 α = 90 b = 58.853 β = 90 c = 60.886 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 150 M SINGLE WAVELENGTH 2 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C 2 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
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 1.07 50 93.9 0.062 28.2 6.2 72978
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 1.07 1.11 82.8 0.332 2.9 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB ENTRY 7HVP 1.07 10 75585 3830 93.9 0.144 0.143 0.184 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 44 1379.92 1791.98
RMS Deviations Key Refinement Restraint Deviation s_zero_chiral_vol 0.106 s_approx_iso_adps 0.098 s_non_zero_chiral_vol 0.087 s_similar_adp_cmpnt 0.061 s_anti_bump_dis_restr 0.043 s_angle_d 0.039 s_from_restr_planes 0.035 s_bond_d 0.016 s_rigid_bond_adp_cmpnt 0.007 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1567 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 59
Software Software Software Name Purpose SHELXL-97 refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing