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I84V HIV-1 protease in complex with a amino decorated pyrrolidine-based inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PWC PDB entry 2PWC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 2.5M NaCl, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.652382 53.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.336 α = 90 b = 85.763 β = 90 c = 46.56 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 113 IMAGE PLATE RIGAKU RAXIS IV 2006-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.92 25 98.6 0.091 0.091 15.8 4.3 17926 22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.92 1.95 97 0.463 0.463 3.2 4.3 877
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB entry 2PWC 1.92 10 2 4 16879 16879 893 93.8 0.2012 0.18 0.1784 0.1901 0.2306 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 1553 1636
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.063 s_non_zero_chiral_vol 0.036 s_zero_chiral_vol 0.028 s_from_restr_planes 0.0239 s_angle_d 0.022 s_anti_bump_dis_restr 0.009 s_bond_d 0.005 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1486 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 42
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing