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Crystal Structure of multi-drug resistant HIV-1 protease PR-S17 with substrate analog CA-p2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 298 2.1M Sodium chloride, 0.1M HEPES pH 7.6
Crystal Properties Matthews coefficient Solvent content 2.5 50.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.704 α = 90 b = 60.358 β = 90.93 c = 66.476 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 300 mm CCD 2016-02-28 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) 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 1.7 50 99.5 0.076 0.045 17.1 3.9 46434
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 99.6 0.418 0.418 0.242 0.886 6.1 3.8
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 5T2Z 1.7 34.53 44127 2291 99.2 0.17766 0.17581 0.1849 0.21179 0.2146 RANDOM 21.102
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] -0.38 -0.58 -0.13 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.299 r_dihedral_angle_3_deg 12.091 r_dihedral_angle_4_deg 10.947 r_dihedral_angle_1_deg 7.099 r_long_range_B_other 6.449 r_long_range_B_refined 6.447 r_scangle_other 5.401 r_scbond_it 3.609 r_scbond_other 3.608 r_angle_other_deg 3.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.299 r_dihedral_angle_3_deg 12.091 r_dihedral_angle_4_deg 10.947 r_dihedral_angle_1_deg 7.099 r_long_range_B_other 6.449 r_long_range_B_refined 6.447 r_scangle_other 5.401 r_scbond_it 3.609 r_scbond_other 3.608 r_angle_other_deg 3.595 r_mcangle_it 3.018 r_mcangle_other 3.017 r_angle_refined_deg 2.218 r_mcbond_it 2.133 r_mcbond_other 2.132 r_chiral_restr 0.141 r_bond_refined_d 0.024 r_gen_planes_other 0.02 r_gen_planes_refined 0.013 r_bond_other_d 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 3044 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing