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Crystal Structure of multi-drug resistant HIV-1 protease PR-S17 (D25N)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 1.95 M sodium chloride, 0.1 M Bis-Tris, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.86 56.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.645 α = 90 b = 49.645 β = 90 c = 86.703 γ = 120
Symmetry Space Group P 32 2 1
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 2017-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.21 50 91.9 0.071 0.035 18.7 5 35459 14.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.21 1.25 52.1 0.425 0.318 0.751 2 2.1
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 FREE R-VALUE 5T2E 1.21 38.55 33739 1701 91.96 0.14854 0.14776 0.1481 0.16411 0.1643 Random 20.01
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] -0.01 -0.01 -0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.451 r_dihedral_angle_4_deg 10.584 r_dihedral_angle_3_deg 9.669 r_dihedral_angle_1_deg 6.704 r_rigid_bond_restr 6.647 r_long_range_B_refined 6.253 r_long_range_B_other 6.207 r_mcangle_it 5.73 r_mcangle_other 5.725 r_scangle_other 4.768
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.451 r_dihedral_angle_4_deg 10.584 r_dihedral_angle_3_deg 9.669 r_dihedral_angle_1_deg 6.704 r_rigid_bond_restr 6.647 r_long_range_B_refined 6.253 r_long_range_B_other 6.207 r_mcangle_it 5.73 r_mcangle_other 5.725 r_scangle_other 4.768 r_scbond_it 4.556 r_scbond_other 4.556 r_mcbond_other 4.437 r_mcbond_it 4.432 r_angle_refined_deg 2.007 r_angle_other_deg 1.434 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 761 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing SHELXL refinement HKL-2000 data reduction