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Crystal Structure of HIV-1 Protease Inhibitor GRL-105-11A Containing Substituted fused-Tetrahydropyranyl Tetrahydrofuran as P2-Ligand
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 5.5 298 1.3M NaCl, 0.1M Sodium Acetate buffer (pH 5.5)
Crystal Properties Matthews coefficient Solvent content 2.7 54.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.677 α = 90 b = 86.055 β = 90 c = 46.003 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 225 mm CCD 2013-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 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 1.62 50 96.8 0.057 30.9 7 29447
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 1.62 1.68 90 0.483 3.9 6.1
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-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-VALUE 3NU3 1.62 50 29405 29447 1472 96.9 0.2031 0.201 0.1792 0.2454 0.2233 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 20 1679.2
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.061 s_non_zero_chiral_vol 0.056 s_zero_chiral_vol 0.043 s_from_restr_planes 0.025 s_angle_d 0.024 s_anti_bump_dis_restr 0.009 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 1512 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 43
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing SHELXL-97 refinement