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Crystal Structure of P. aeruginosa LpxC with N-Hydroxyformamide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1.6 M AmSO4, 0.5 M LiCl
Crystal Properties Matthews coefficient Solvent content 2 38.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.621 α = 90 b = 157.351 β = 101.64 c = 48.846 γ = 90
Symmetry Space Group P 1 21 1
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 315r 2019-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97926 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2 50 97.6 0.116 0.13 0.057 5.2 4.7 34441
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 91.3 0.433 0.493 0.23 0.841 4
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 5u39 2 47.89 32662 1744 97.55 0.1684 0.1656 0.1745 0.2221 0.2235 RANDOM 31.885
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] -1.84 1.2 -2.06 3.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.367 r_dihedral_angle_4_deg 16.257 r_dihedral_angle_3_deg 16.144 r_dihedral_angle_1_deg 7.271 r_angle_refined_deg 1.496 r_angle_other_deg 1.264 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.367 r_dihedral_angle_4_deg 16.257 r_dihedral_angle_3_deg 16.144 r_dihedral_angle_1_deg 7.271 r_angle_refined_deg 1.496 r_angle_other_deg 1.264 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4660 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 139
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction MOLREP phasing