☰ Navigation Tabs
HIV-1 wild type protease with GRL-110-19A, a chloroacetamide derivative based on Darunavir as P2' group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VOD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 0.65 M NaCl, 0.1 M Sodium Acetate, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.7 54.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.419 α = 90 b = 86.235 β = 90 c = 46.075 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 MX300-HS 2019-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
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 1.29 50 95.4 0.052 0.057 0.021 14.5 6.8 56469
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 1.29 1.34 69.8 0.639 0.739 0.358 0.704 3.6
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 6VOD 1.29 34.72 53658 2771 95.28 0.1331 0.1316 0.1305 0.1626 0.1622 RANDOM 14.078
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] -0.15 -0.46 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.893 r_dihedral_angle_1_deg 6.941 r_dihedral_angle_2_deg 5.041 r_rigid_bond_restr 4.802 r_angle_refined_deg 1.926 r_angle_other_deg 0.677 r_chiral_restr 0.133 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.893 r_dihedral_angle_1_deg 6.941 r_dihedral_angle_2_deg 5.041 r_rigid_bond_restr 4.802 r_angle_refined_deg 1.926 r_angle_other_deg 0.677 r_chiral_restr 0.133 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.008 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 92
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction