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Crystal structure of wild-type HIV-1 protease in complex with AG23
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 2.04 39.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.386 α = 90 b = 57.33 β = 90 c = 61.097 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 315 2010-01-20 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 1.65 50 96.5 0.057 13.2 4.9 21177
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 1.65 1.71 97.2 0.356 4.8 2089
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1F7A 1.65 41.81 21153 1080 96.56 0.1737 0.1722 0.203 0.2592 RANDOM 25.181
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] -1.09 -0.3 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.586 r_dihedral_angle_4_deg 14.748 r_dihedral_angle_3_deg 12.829 r_dihedral_angle_1_deg 6.584 r_scangle_it 2.732 r_scbond_it 1.846 r_angle_refined_deg 1.434 r_mcangle_it 1.065 r_angle_other_deg 0.826 r_mcbond_it 0.609
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.586 r_dihedral_angle_4_deg 14.748 r_dihedral_angle_3_deg 12.829 r_dihedral_angle_1_deg 6.584 r_scangle_it 2.732 r_scbond_it 1.846 r_angle_refined_deg 1.434 r_mcangle_it 1.065 r_angle_other_deg 0.826 r_mcbond_it 0.609 r_mcbond_other 0.16 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1494 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 58
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction AMoRE phasing