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X-ray structure of HIV-1 protease and hydrated form of ketomethylene isostere inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HVP PDB ENTRY 4HVP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1M CITRATE, 0.2M SODIUM PHOPHATE, 30% (W/V) AMMONIUM SULFATE, 10% (V/V) DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.2 α = 90 b = 58.077 β = 90 c = 61.658 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 110 CCD MARMOSAIC 300 mm CCD Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geometry 2007-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03320 APS 23-ID-B
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 1.4 50 99.9 0.084 32 6.8 37058 37029
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 1.4 1.45 99.9 0.384 6.3 6.4 3623
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 4HVP 1.4 20 36899 1846 99.66 0.204 0.204 0.202 0.215 0.2098 RANDOM 11.995
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] 0.87 -0.25 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.277 r_dihedral_angle_4_deg 15.947 r_dihedral_angle_3_deg 10.04 r_dihedral_angle_1_deg 6.165 r_scangle_it 4.091 r_scbond_it 2.715 r_mcangle_it 1.858 r_angle_refined_deg 1.684 r_mcbond_it 1.264 r_angle_other_deg 0.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.277 r_dihedral_angle_4_deg 15.947 r_dihedral_angle_3_deg 10.04 r_dihedral_angle_1_deg 6.165 r_scangle_it 4.091 r_scbond_it 2.715 r_mcangle_it 1.858 r_angle_refined_deg 1.684 r_mcbond_it 1.264 r_angle_other_deg 0.905 r_nbd_refined 0.339 r_mcbond_other 0.338 r_nbd_other 0.198 r_symmetry_vdw_other 0.17 r_nbtor_refined 0.169 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.156 r_symmetry_vdw_refined 0.121 r_chiral_restr 0.102 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1518 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 56
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Locally data collection HKL-2000 data reduction MOLREP phasing