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Crystal Structure of multi-drug resistant HIV-1 protease PR-S17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UF3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 298 2.1M sodium chloride and 0.1M HEPES pH7.6
Crystal Properties Matthews coefficient Solvent content 2.88 57.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.899 α = 90 b = 49.899 β = 90 c = 86.628 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 MARMOSAIC 300 mm CCD Mirrors 2015-10-26 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) 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 1.5 50 99.5 0.057 25.22 5.6 20429
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 99.5 0.447 0.849 3.09 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 3UF3 1.5 30.59 19390 1001 99.41 0.13986 0.13752 0.1369 0.18552 0.1869 RANDOM 26.231
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] 0.23 0.11 0.23 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.904 r_sphericity_free 23.813 r_sphericity_bonded 11.55 r_dihedral_angle_4_deg 10.645 r_dihedral_angle_3_deg 9.849 r_rigid_bond_restr 7.25 r_dihedral_angle_1_deg 6.238 r_long_range_B_refined 4.986 r_scangle_other 4.935 r_long_range_B_other 4.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.904 r_sphericity_free 23.813 r_sphericity_bonded 11.55 r_dihedral_angle_4_deg 10.645 r_dihedral_angle_3_deg 9.849 r_rigid_bond_restr 7.25 r_dihedral_angle_1_deg 6.238 r_long_range_B_refined 4.986 r_scangle_other 4.935 r_long_range_B_other 4.805 r_scbond_it 4.328 r_scbond_other 4.328 r_mcangle_it 3.584 r_mcangle_other 3.582 r_mcbond_other 3.077 r_mcbond_it 3.076 r_angle_refined_deg 2.556 r_angle_other_deg 1.353 r_chiral_restr 0.183 r_bond_refined_d 0.031 r_gen_planes_refined 0.014 r_gen_planes_other 0.007 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 761 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing