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HIV-1 wild type protease with GRL-042-17A, 3-phenylhexahydro-2h-cyclopenta[d]oxazol-2-one with a bicyclic oxazolidinone scaffold 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 5.5 298 1.4M NACL, 0.1M SODIUM ACETATE PH
5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.75 55.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.793 α = 90 b = 86.043 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 CCD RAYONIX MX300HE 2017-10-25 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) 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 1.3 50 92.1 0.082 19.7 6.7 54309
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 1.3 1.35 53 0.506 2.1 2.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3NU3 1.3 49.1 51484 2772 92.01 0.14971 0.14792 0.18234 0.1985 RANDOM 22.151
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] -1.62 1.13 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.093 r_sphericity_free 23.033 r_sphericity_bonded 21.7 r_dihedral_angle_4_deg 17.827 r_dihedral_angle_3_deg 11.687 r_dihedral_angle_1_deg 6.392 r_rigid_bond_restr 5.609 r_long_range_B_refined 5.029 r_long_range_B_other 5.029 r_scangle_other 4.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.093 r_sphericity_free 23.033 r_sphericity_bonded 21.7 r_dihedral_angle_4_deg 17.827 r_dihedral_angle_3_deg 11.687 r_dihedral_angle_1_deg 6.392 r_rigid_bond_restr 5.609 r_long_range_B_refined 5.029 r_long_range_B_other 5.029 r_scangle_other 4.986 r_scbond_it 4.857 r_scbond_other 4.854 r_mcangle_it 2.954 r_mcangle_other 2.954 r_mcbond_it 2.469 r_mcbond_other 2.434 r_angle_refined_deg 1.947 r_angle_other_deg 1.036 r_chiral_restr 0.136 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing SHELXL refinement HKL-2000 data reduction