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HIV-1 wild type protease with GRL-00819A, with phenyl-boronic-acid as P2'-ligand and with a 6-5-5-ring fused crown-like tetrahydropyranofuran as the 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 6 298 1.4 M sodium chloride, 0.1 M sodium acetate buffer pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.72 54.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.921 α = 90 b = 86.479 β = 90 c = 45.875 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 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 1.33 50 98.9 0.061 0.067 0.027 12.8 6 53993
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 1.33 1.38 94.1 0.749 0.842 0.376 0.713 4.3
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 FREE R-VALUE 3NU3 1.33 33.41 51313 2635 98.82 0.1391 0.1372 0.1453 0.1772 0.1424 RANDOM 18.536
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] -2.04 -0.16 2.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.567 r_dihedral_angle_4_deg 16.376 r_dihedral_angle_3_deg 11.948 r_dihedral_angle_1_deg 7.002 r_rigid_bond_restr 5.036 r_angle_refined_deg 2.331 r_angle_other_deg 1.503 r_chiral_restr 0.451 r_bond_refined_d 0.02 r_gen_planes_refined 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.567 r_dihedral_angle_4_deg 16.376 r_dihedral_angle_3_deg 11.948 r_dihedral_angle_1_deg 7.002 r_rigid_bond_restr 5.036 r_angle_refined_deg 2.331 r_angle_other_deg 1.503 r_chiral_restr 0.451 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 98
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction