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X-ray crystal structure of darunavir-resistant HIV-1 protease (P51) in complex with GRL-001
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 298 0.15 M (NH4)2SO4, 0.1 M HEPES (pH 7.2), 20% (v/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 2.17 43.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.071 α = 90 b = 63.071 β = 90 c = 82.196 γ = 120
Symmetry Space Group P 61 2 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 PILATUS 6M 2016-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.21 54.62 96.3 22.32 14.3 28980
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.21 1.25
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 5TYR 1.21 54.62 27537 1393 96.14 0.19265 0.192 0.1922 0.206 0.2054 RANDOM 16.02
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] 0.16 0.08 0.16 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.795 r_dihedral_angle_3_deg 9.806 r_dihedral_angle_1_deg 7.801 r_long_range_B_other 5.337 r_long_range_B_refined 5.334 r_scangle_other 4.065 r_dihedral_angle_4_deg 3.851 r_scbond_it 2.612 r_scbond_other 2.612 r_mcangle_other 2.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.795 r_dihedral_angle_3_deg 9.806 r_dihedral_angle_1_deg 7.801 r_long_range_B_other 5.337 r_long_range_B_refined 5.334 r_scangle_other 4.065 r_dihedral_angle_4_deg 3.851 r_scbond_it 2.612 r_scbond_other 2.612 r_mcangle_other 2.462 r_mcangle_it 2.46 r_angle_refined_deg 2.124 r_angle_other_deg 1.995 r_mcbond_it 1.598 r_mcbond_other 1.586 r_chiral_restr 0.124 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.009 r_gen_planes_other 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 764 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing