☰ Navigation Tabs
HIV-1 wild type protease with GRL-03419A, with N-(2,5-dimethylphenyl)-4-(pyridin-3-yl)pyrimidin-2-amine as P2-P3 group and 3,5-difluorophenylmethyl as the P1 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 6 298 0.57M sodium chloride and 0.1 M sodium acetate, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.7 54.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.609 α = 90 b = 86.214 β = 90 c = 46.189 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 2021-06-05 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 1.12 50 93.4 0.068 16.9 5.5 84494 6.894
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 1.12 1.16 56.1 0.337 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.12 36.3 80315 4124 93.35 0.12135 0.1206 0.1203 0.13584 0.1353 RANDOM 10.509
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] 0.33 -0.21 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.346 r_dihedral_angle_1_deg 6.914 r_rigid_bond_restr 5.643 r_dihedral_angle_2_deg 4.265 r_scangle_other 3.276 r_long_range_B_refined 3.149 r_long_range_B_other 3.004 r_scbond_it 2.905 r_scbond_other 2.901 r_angle_refined_deg 1.943
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.346 r_dihedral_angle_1_deg 6.914 r_rigid_bond_restr 5.643 r_dihedral_angle_2_deg 4.265 r_scangle_other 3.276 r_long_range_B_refined 3.149 r_long_range_B_other 3.004 r_scbond_it 2.905 r_scbond_other 2.901 r_angle_refined_deg 1.943 r_mcangle_it 1.72 r_mcangle_other 1.72 r_mcbond_it 1.307 r_mcbond_other 1.307 r_angle_other_deg 0.782 r_chiral_restr 0.128 r_gen_planes_other 0.016 r_bond_refined_d 0.014 r_gen_planes_refined 0.014 r_bond_other_d 0.004 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 312 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing PDB_EXTRACT data extraction