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Crystal structure of Wild-type HIV-1 protease in complex With AF68
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F7A PDB ENTRY 1F7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 HANGING DROP, VAPOR DIFFUSION 6.2 295 24-29% ammonium sulfate, 63 mM sodium citrate, 126 mM phosphate buffer, pH 6.2, HANGING DROP, VAPOR DIFFUSION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.07 40.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.739 α = 90 b = 57.52 β = 90 c = 61.483 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 100 CCD ADSC QUANTUM 4 2009-12-17 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 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 1.7 50 95.5 0.07 11.2 6.1 19391
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 1.7 1.76 95.9 0.316 6.2 1895
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 1F7A 1.7 42 19310 990 95.21 0.1755 0.1735 0.1838 0.2139 0.2206 RANDOM 20.3054
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] -1.67 0.58 1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.193 r_dihedral_angle_4_deg 19.709 r_dihedral_angle_3_deg 11.258 r_dihedral_angle_1_deg 6.268 r_scangle_it 2.612 r_scbond_it 1.596 r_angle_refined_deg 1.223 r_mcangle_it 0.894 r_angle_other_deg 0.795 r_mcbond_it 0.482
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.193 r_dihedral_angle_4_deg 19.709 r_dihedral_angle_3_deg 11.258 r_dihedral_angle_1_deg 6.268 r_scangle_it 2.612 r_scbond_it 1.596 r_angle_refined_deg 1.223 r_mcangle_it 0.894 r_angle_other_deg 0.795 r_mcbond_it 0.482 r_mcbond_other 0.136 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1498 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 48
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction BioCARS-developed data collection HKL-2000 data reduction AMoRE phasing