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Crystal Structures of Multidrug-resistant HIV-1 Protease in Complex with Mechanism-Based Aspartyl Protease Inhibitors.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TW7 PDB ENTRY 1TW7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 298 0.3 M NaCl, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.48 50.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.727 α = 90 b = 45.727 β = 90 c = 102.149 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD MAR CCD 165 mm 2008-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 1.0 APS 21-ID-F
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 1.7 50 0.04 22795
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 1.7 1.76 100
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 PDB ENTRY 1TW7 1.7 18.98 21607 1169 99.46 0.20026 0.19786 0.1979 0.24539 0.2446 RANDOM 24.058
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] -0.02 -0.02 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.726 r_dihedral_angle_4_deg 13.731 r_dihedral_angle_3_deg 12.866 r_dihedral_angle_1_deg 6.022 r_scangle_it 3.942 r_scbond_it 2.459 r_mcangle_it 1.78 r_angle_refined_deg 1.5 r_mcbond_it 1.155 r_angle_other_deg 0.367
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.726 r_dihedral_angle_4_deg 13.731 r_dihedral_angle_3_deg 12.866 r_dihedral_angle_1_deg 6.022 r_scangle_it 3.942 r_scbond_it 2.459 r_mcangle_it 1.78 r_angle_refined_deg 1.5 r_mcbond_it 1.155 r_angle_other_deg 0.367 r_nbtor_refined 0.308 r_symmetry_vdw_other 0.251 r_symmetry_vdw_refined 0.244 r_symmetry_hbond_refined 0.22 r_nbd_refined 0.197 r_nbd_other 0.169 r_xyhbond_nbd_refined 0.155 r_nbtor_other 0.099 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 44
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling