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X-ray crystal structure of wild type HIV-1 protease in complex with GRL-063
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 7 298 0.15 M Ammonium sulfate, 0.1 M HEPES (pH 7.0), 20% (w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 2.18 43.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.087 α = 90 b = 63.087 β = 90 c = 82.339 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 2016-12-02 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 1.53 54.63 100 15.33 18.5 15238
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 1.53 1.58
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 1.53 1.58 14441 759 99.96 0.22078 0.2186 0.2323 0.2623 0.2648 RANDOM 24.97
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] 0.22 0.11 0.22 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.435 r_dihedral_angle_4_deg 12.954 r_dihedral_angle_3_deg 10.742 r_dihedral_angle_1_deg 8.106 r_long_range_B_refined 5.239 r_long_range_B_other 5.237 r_scangle_other 4.126 r_mcangle_it 2.794 r_mcangle_other 2.794 r_scbond_it 2.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.435 r_dihedral_angle_4_deg 12.954 r_dihedral_angle_3_deg 10.742 r_dihedral_angle_1_deg 8.106 r_long_range_B_refined 5.239 r_long_range_B_other 5.237 r_scangle_other 4.126 r_mcangle_it 2.794 r_mcangle_other 2.794 r_scbond_it 2.741 r_scbond_other 2.738 r_angle_refined_deg 2.072 r_mcbond_it 1.997 r_mcbond_other 1.99 r_angle_other_deg 1.951 r_chiral_restr 0.113 r_bond_refined_d 0.024 r_gen_planes_refined 0.014 r_gen_planes_other 0.009 r_bond_other_d 0.007 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 760 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing