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Crystal structure of Pseudomonas aeruginosa LpxA in complex with compound 45
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 278 1.6 M (NH4)2SO4, 10% 1,4-Dioxane, 0.1 M MES pH 6.7
Crystal Properties Matthews coefficient Solvent content 5.53 77.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 378.61 α = 90 b = 378.61 β = 90 c = 264.64 γ = 90
Symmetry Space Group P 42 21 2
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 EIGER2 X 16M 2019-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.58 109.08 100 0.615 0.626 0.118 0.994 7.3 27.8 223901 95.6
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 3.58 3.67 100 3.469 3.53 0.654 0.592 29
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 5DEM 3.58 109.08 212833 10979 99.98 0.1954 0.1945 0.1962 0.2122 0.2119 RANDOM 95.596
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] -0.36 -0.36 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.642 r_dihedral_angle_4_deg 21.531 r_dihedral_angle_3_deg 21.4 r_dihedral_angle_1_deg 9.124 r_angle_refined_deg 2.287 r_angle_other_deg 1.385 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.642 r_dihedral_angle_4_deg 21.531 r_dihedral_angle_3_deg 21.4 r_dihedral_angle_1_deg 9.124 r_angle_refined_deg 2.287 r_angle_other_deg 1.385 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 59100 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 1106
Software Software Software Name Purpose Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction