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HIV-1 protease in complex with a dimethylallyl decorated pyrrolidine based inhibitor (orthorombic space group)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PQZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 3.5M NaCl, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.126596 42.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.018 α = 90 b = 57.581 β = 90 c = 61.365 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 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 98.8 0.052 0.052 26.1 4.4 22526 15.9
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 89.4 0.35 0.35 2.7 2.5 993
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 MOLECULAR REPLACEMENT FREE R 2PQZ 1.65 10 2 4 21271 21271 1118 93.9 0.2018 0.185 0.183 0.1872 0.239 0.1994 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 1 1554 1650
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.063 s_non_zero_chiral_vol 0.042 s_zero_chiral_vol 0.04 s_from_restr_planes 0.0265 s_angle_d 0.024 s_anti_bump_dis_restr 0.017 s_bond_d 0.007 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1483 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 43
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing