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Structure of human neutrophil elastase in complex with a 5,8-dihydro[1,2,4]triazolo[4,3-a]pyrimidin-3(2H)-one inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q77
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 18% PEG-3350, 0.2M ammonium citrate
Crystal Properties Matthews coefficient Solvent content 2.32 47.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.16 α = 90 b = 73.16 β = 90 c = 70.15 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 PIXEL DECTRIS PILATUS 6M 2014-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 1.14 36.61 78.8 0.035 33.7 8.8 61016
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 1.14 1.17 0.329
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 1.14 36.61 57914 3094 78.65 0.13507 0.13402 0.1395 0.1549 0.1586 RANDOM 19.267
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] 0.25 0.12 0.25 -0.8
RMS Deviations Key Refinement Restraint Deviation r_scangle_other 20.985 r_scbond_other 20.399 r_scbond_it 19.979 r_long_range_B_refined 18.902 r_long_range_B_other 18.815 r_dihedral_angle_3_deg 12.952 r_mcangle_other 9.615 r_mcangle_it 9.577 r_dihedral_angle_1_deg 7.538 r_mcbond_it 7.179
RMS Deviations Key Refinement Restraint Deviation r_scangle_other 20.985 r_scbond_other 20.399 r_scbond_it 19.979 r_long_range_B_refined 18.902 r_long_range_B_other 18.815 r_dihedral_angle_3_deg 12.952 r_mcangle_other 9.615 r_mcangle_it 9.577 r_dihedral_angle_1_deg 7.538 r_mcbond_it 7.179 r_mcbond_other 7.156 r_rigid_bond_restr 4.39 r_angle_refined_deg 1.403 r_angle_other_deg 0.504 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1636 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 115
Software Software Software Name Purpose PDB-REDO refinement PHASER phasing xia2 data scaling Coot model building autoPROC data reduction