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Structure of wild-type HIV protease in complex with darunavir
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 RESERVOIR: 2 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, PH 4.6. DROPS: 2 UL PROTEIN + 1UL RESERVOIR, PROTEIN CONCENTRATION 5MG/ML, 5-FOLD MOLAR EXCESS OF INHIBITOR (DISSOLVED IN DMSO) OVER PROTEIN, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K
Crystal Properties Matthews coefficient Solvent content 2.12 41.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.557 α = 90 b = 62.557 β = 90 c = 81.523 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 MARMOSAIC 225 mm CCD 2009-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 EMBL/DESY, HAMBURG X12
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 1.95 50 99.9 0.06 26.45 6.7 13257
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 1.95 2.02 99.9 0.513 2.7 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.95 27.09 12558 662 99.95 0.18523 0.18288 0.1821 0.23 0.2286 RANDOM 36.773
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 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.981 r_dihedral_angle_4_deg 18.813 r_dihedral_angle_3_deg 14.079 r_dihedral_angle_1_deg 6.332 r_scangle_it 3.084 r_scbond_it 1.908 r_angle_refined_deg 1.508 r_mcangle_it 1.301 r_mcbond_it 1.296 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.981 r_dihedral_angle_4_deg 18.813 r_dihedral_angle_3_deg 14.079 r_dihedral_angle_1_deg 6.332 r_scangle_it 3.084 r_scbond_it 1.908 r_angle_refined_deg 1.508 r_mcangle_it 1.301 r_mcbond_it 1.296 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.233 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.171 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1520 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 76
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling