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Crystal structure analysis of HIV-1 protease with a substrate analog P2-NC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AOC PDB Entry 2AOC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 293 AMMONIUM SULFATE 17%, CITRATE PHOSPHATE BUFFER PH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.996 α = 90 b = 85.78 β = 90 c = 46.532 γ = 90
Symmetry Space Group P 21 21 2
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 MAR CCD 165 mm 2003-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 95.5 0.101 8.9 6.1 46637
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 66.6 0.456 2.06 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB Entry 2AOC 1.4 10 44291 35279 2210 95.6 0.1566 0.1544 0.1964 0.1864 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 23 1663 1765.03
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.085 s_non_zero_chiral_vol 0.063 s_zero_chiral_vol 0.06 s_anti_bump_dis_restr 0.048 s_similar_adp_cmpnt 0.034 s_from_restr_planes 0.0295 s_angle_d 0.029 s_bond_d 0.011 s_rigid_bond_adp_cmpnt 0.003 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 77
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling HKL-2000 data reduction SHELX model building SHELXL-97 refinement HKL-2000 data scaling SHELX phasing