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Crystal structure of wild-type HIV-1 protease in complex with AF72
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 2.11 41.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.893 α = 90 b = 58.004 β = 90 c = 61.742 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 IMAGE PLATE RIGAKU RAXIS IV 2009-06-12 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 1.8 50 94.2 0.054 13.2 7 16543
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 1.8 1.86 77.9 0.383 5.6 1344
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 1.8 42.27 16511 829 94.29 0.178 0.1762 0.1941 0.2128 0.2319 RANDOM 26.397
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] -0.45 0.12 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.489 r_dihedral_angle_4_deg 17.29 r_dihedral_angle_3_deg 12.294 r_dihedral_angle_1_deg 6.232 r_scangle_it 2.314 r_scbond_it 1.468 r_angle_refined_deg 1.366 r_mcangle_it 0.931 r_angle_other_deg 0.842 r_mcbond_it 0.547
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.489 r_dihedral_angle_4_deg 17.29 r_dihedral_angle_3_deg 12.294 r_dihedral_angle_1_deg 6.232 r_scangle_it 2.314 r_scbond_it 1.468 r_angle_refined_deg 1.366 r_mcangle_it 0.931 r_angle_other_deg 0.842 r_mcbond_it 0.547 r_mcbond_other 0.153 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1494 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 59
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing