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HIV-1 wild type protease with GRL-026-18A, a crown-like tetrahydropyranotetrahydrofuran with a bridged methylene group as a 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 6.2 298 1.8 M sodium chloride, 0.1 M sodium acetate pH 6.2; Starting protein concentration was 4.2 mg/mL and inhibitors were complexed at 5:1 molar ratio
Crystal Properties Matthews coefficient Solvent content 2.72 54.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.904 α = 90 b = 86.207 β = 90 c = 46.09 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 90 PIXEL DECTRIS EIGER X 16M 2019-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.18 50 93.6 0.082 0.09 0.035 12.2 5.6 72509
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.18 1.22 55.5 0.358 0.441 0.251 0.8 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 THROUGHOUT 3NU3 1.18 33.48 68939 3516 93.36 0.1365 0.1356 0.145 0.1553 0.1643 RANDOM 15.273
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] -1.47 -0.42 1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.984 r_dihedral_angle_4_deg 18.507 r_dihedral_angle_3_deg 11.256 r_rigid_bond_restr 7.633 r_dihedral_angle_1_deg 6.803 r_angle_refined_deg 2.559 r_angle_other_deg 1.715 r_chiral_restr 0.256 r_bond_refined_d 0.021 r_gen_planes_refined 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.984 r_dihedral_angle_4_deg 18.507 r_dihedral_angle_3_deg 11.256 r_rigid_bond_restr 7.633 r_dihedral_angle_1_deg 6.803 r_angle_refined_deg 2.559 r_angle_other_deg 1.715 r_chiral_restr 0.256 r_bond_refined_d 0.021 r_gen_planes_refined 0.013 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction