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Crystal Structure of a Nelfinavir Resistant HIV-1 CRF01_AE Protease variant (N88S) in Complex with the Protease Inhibitor Darunavir.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TSU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 295 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 18-33% Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.11 41.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.878 α = 90 b = 61.878 β = 90 c = 82.15 γ = 120
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 ADSC QUANTUM 315 bent conical Si, Rh coating 2008-11-07 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.90 APS 14-BM-C
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 1.76 53.61 97.4 0.041 19.6 4.6 79445
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.76 1.82 79.4 0.401 2.6 1408
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1TSU 1.76 53.61 79445 872 98 0.198 0.196 0.2348 0.239 0.2662 RANDOM 33.054
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] 0.34 0.17 0.34 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.829 r_dihedral_angle_4_deg 13.27 r_dihedral_angle_3_deg 12.438 r_dihedral_angle_1_deg 8.2 r_scangle_it 2.909 r_scbond_it 2.227 r_angle_refined_deg 1.7 r_mcangle_it 1.403 r_mcbond_it 1.207 r_angle_other_deg 0.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.829 r_dihedral_angle_4_deg 13.27 r_dihedral_angle_3_deg 12.438 r_dihedral_angle_1_deg 8.2 r_scangle_it 2.909 r_scbond_it 2.227 r_angle_refined_deg 1.7 r_mcangle_it 1.403 r_mcbond_it 1.207 r_angle_other_deg 0.899 r_mcbond_other 0.253 r_nbd_refined 0.21 r_nbd_other 0.206 r_symmetry_vdw_other 0.188 r_nbtor_refined 0.176 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.105 r_chiral_restr 0.098 r_nbtor_other 0.088 r_xyhbond_nbd_other 0.017 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1463 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 58
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction BioCARS data collection HKL-2000 data reduction