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Crystal structure of wild-type HIV-1 protease with C3-Substituted Hexahydrocyclopentafuranyl Urethane as P2-Ligand, GRL-0489A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NU3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 298 1.2 M ammonium chloride, 0.1 M sodium acetate buffer, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.7 54.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.39 α = 90 b = 86.552 β = 90 c = 45.846 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 MAR SCANNER 225 MM PLATE 2011-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1 APS 22-BM
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 1.45 50 98.4 0.072 16 4.6 41487 41487 16.8
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 1.45 1.5 88.5 0.418 2 2.4
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 3NU3 1.45 10 41189 41189 2055 98.6 0.1599 0.1565 0.1565 0.1628 0.2192 0.2115 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 26 1638 1667.75
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.073 s_non_zero_chiral_vol 0.057 s_zero_chiral_vol 0.054 s_similar_adp_cmpnt 0.053 s_from_restr_planes 0.0295 s_angle_d 0.029 s_anti_bump_dis_restr 0.025 s_bond_d 0.01 s_rigid_bond_adp_cmpnt 0.003 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 42
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling