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HIV-1 protease in complex with a dimethylallyl decorated pyrrolidine based inhibitor (hexagonal space group)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PQZ 2PQZ(monomer)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 3M NaCl, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 42.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.625 α = 90 b = 62.625 β = 90 c = 82.303 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 196 CCD MAR CCD 165 mm double crystal monochromator with two sets of mirrors 2007-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 1.65 25 97.8 0.08 0.08 23.2 6.9 11774 11774 24.8
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 1.65 1.68 96.2 0.386 0.386 4.3 5.5 559
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION AB INITIO FREE R 2PQZ(monomer) 1.65 10 2 4 11127 11127 593 93.3 0.2342 0.225 0.224 0.2292 0.274 0.2371 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 778 798
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.071 s_non_zero_chiral_vol 0.04 s_zero_chiral_vol 0.035 s_from_restr_planes 0.0286 s_angle_d 0.023 s_bond_d 0.007 s_similar_dist s_anti_bump_dis_restr s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 738 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 21
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing