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Crystal structure of wild-type HIV-1 protease with new oxatricyclic designed inhibitor GRL-0519A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QCI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 298 1.18 M NaCl, 0.1 M Acetate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.3 54.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.546 α = 90 b = 86.212 β = 90 c = 45.635 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 MARMOSAIC 300 mm CCD 2009-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.8 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 1.27 50 90.5 0.067 15.8 3.8 55825 55825 13.869
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) 1.27 1.32 54.7 0.334 2.1 2 3300
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION Phaser FREE R 2QCI 1.27 10 55721 55721 2789 90.6 0.1476 0.1452 0.1452 0.1533 0.1892 0.194 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 48 1644 1689.5
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.076 s_non_zero_chiral_vol 0.072 s_zero_chiral_vol 0.064 s_anti_bump_dis_restr 0.059 s_similar_adp_cmpnt 0.054 s_angle_d 0.033 s_from_restr_planes 0.032 s_bond_d 0.012 s_rigid_bond_adp_cmpnt 0.004 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 62
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling