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Crystal Structure of HIV-1 Protease Inhibitors Containing Substituted fused-Tetrahydropyranyl Tetrahydrofuran as P2-Ligand GRL-004-11A
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 4.6 298 1.18M NaCl, 0.1M NaAcetate, pH=4.6
Crystal Properties Matthews coefficient Solvent content 2.71 54.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.642 α = 90 b = 86.329 β = 90 c = 45.981 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 2013-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.8 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 1.22 50 93.1 0.068 22.9 7.2 65344
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 1.22 1.26 54.9 0.357 2.7 3.2
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 1.22 50 65289 65344 3267 93 0.1607 0.159 0.1792 0.2013 0.2053 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 46 1713
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.083 s_approx_iso_adps 0.081 s_zero_chiral_vol 0.07 s_similar_adp_cmpnt 0.053 s_angle_d 0.032 s_from_restr_planes 0.0307 s_anti_bump_dis_restr 0.019 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 195 Heterogen Atoms 42
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing SHELXL-97 refinement