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HIV-1 wild type protease with GRL-02519A, with N-(2,5-dimethylphenyl)-4-(pyridin-3-yl)pyrimidin-2-amine as P2-P3 group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NU3 HIV-1 wild type protease with Amprenavir
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 298 1.1 M NaCl, 0.1 M Sodium Acetate, pH 5.4
Crystal Properties Matthews coefficient Solvent content 2.7 54.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.451 α = 90 b = 86.136 β = 90 c = 46.113 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 2019-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 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 1.25 50 92.1 0.104 11.8 5.5 60036 13.999
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 1.25 1.29 50.1 0.383 1.7
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 1.25 33.4 56906 3079 92.09 0.14083 0.13898 0.1375 0.17555 0.1732 RANDOM 16.194
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] -0.49 -1.08 1.57
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 18.096 r_dihedral_angle_3_deg 12.55 r_dihedral_angle_1_deg 7.019 r_long_range_B_other 6.506 r_long_range_B_refined 6.505 r_scangle_other 5.998 r_scbond_other 5.973 r_scbond_it 5.967 r_dihedral_angle_2_deg 5.363 r_mcangle_it 3.108
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 18.096 r_dihedral_angle_3_deg 12.55 r_dihedral_angle_1_deg 7.019 r_long_range_B_other 6.506 r_long_range_B_refined 6.505 r_scangle_other 5.998 r_scbond_other 5.973 r_scbond_it 5.967 r_dihedral_angle_2_deg 5.363 r_mcangle_it 3.108 r_mcangle_other 3.108 r_mcbond_it 2.436 r_mcbond_other 2.435 r_angle_refined_deg 1.764 r_angle_other_deg 0.671 r_chiral_restr 0.112 r_gen_planes_other 0.019 r_gen_planes_refined 0.013 r_bond_refined_d 0.012 r_bond_other_d 0.007 r_dihedral_angle_4_deg 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 r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction