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Virtual screening approach leading to the identification of a novel and tractable series of Pseudomonas aeruginosa elastase inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EZM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M MOPS pH 6.5 and 1.5M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.07 40.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.122 α = 90 b = 51.26 β = 90 c = 120.708 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 2M 2016-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.977170 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.75 47.226 99.5 0.996 11.9 6.2 28269
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 98 0.591 6.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1EZM 1.75 47.226 28213 1425 99.254 0.21 0.2083 0.2082 0.2399 0.2399 16.918
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] -0.698 0.276 0.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.301 r_dihedral_angle_4_deg 14.675 r_dihedral_angle_3_deg 12.876 r_dihedral_angle_1_deg 6.105 r_lrange_it 5.575 r_lrange_other 5.569 r_scangle_it 4.84 r_scangle_other 4.84 r_scbond_it 3.184 r_scbond_other 3.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.301 r_dihedral_angle_4_deg 14.675 r_dihedral_angle_3_deg 12.876 r_dihedral_angle_1_deg 6.105 r_lrange_it 5.575 r_lrange_other 5.569 r_scangle_it 4.84 r_scangle_other 4.84 r_scbond_it 3.184 r_scbond_other 3.182 r_mcangle_it 2.7 r_mcangle_other 2.699 r_angle_other_deg 2.442 r_mcbond_it 1.91 r_mcbond_other 1.877 r_angle_refined_deg 1.456 r_dihedral_angle_other_2_deg 0.817 r_symmetry_xyhbond_nbd_other 0.268 r_symmetry_nbd_other 0.216 r_symmetry_xyhbond_nbd_refined 0.209 r_nbd_refined 0.201 r_nbd_other 0.184 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.157 r_symmetry_nbd_refined 0.136 r_chiral_restr 0.07 r_symmetry_nbtor_other 0.067 r_metal_ion_refined 0.066 r_bond_other_d 0.037 r_gen_planes_other 0.01 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2296 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing