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Crystal Structure of Wild-type HIV-1 Protease with Cyclopentyltetrahydro- furanyl Urethanes as P2-ligand, GRL-0249A
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 4.8 298 The protein concentration was about 4 mg/ml; 1.2 M NaCl and 0.1 M Acetate Buffer pH 4.8, ratio protein:inhibitor 1:5 and 30% glycerol for cyro protection. VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.69 54.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.58 α = 90 b = 85.93 β = 90 c = 45.99 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 IMAGE PLATE MAR scanner 300 mm plate 2009-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID .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 1.23 50 91.3 0.096 13.8 5.1 62205 62205 11.641
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 1.23 1.27 54.7 0.389 2 1.7 3696
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 MOLECULAR REPLACEMENT FREE R 2QCI 1.23 10 62014 62014 3104 91.2 0.1457 0.1457 0.1437 0.1488 0.1801 0.1773 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 39 1641 1729.3
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.082 s_non_zero_chiral_vol 0.075 s_zero_chiral_vol 0.073 s_similar_adp_cmpnt 0.052 s_angle_d 0.033 s_from_restr_planes 0.0294 s_anti_bump_dis_restr 0.027 s_bond_d 0.013 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 228 Heterogen Atoms 50
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling