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Structure of Pseudomonas aeruginosa FabF mutant C164Q in complex with Platensimycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JB6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.24M NH4HCO2 and 31.2% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.19 43.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.024 α = 90 b = 137.199 β = 90 c = 65.692 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 EIGER X 16M 2019-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.918399 MAX IV BioMAX
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 1.8 68.69 100 0.102 0.118 0.045 0.995 11.05 6.7 71222
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 1.8 1.85 98.6 0.301 0.352 0.135 0.952 4.98 6.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4JB6 1.8 68.69 67633 3510 99.92 0.15882 0.15732 0.18773 0.1946 RANDOM 10.463
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] 0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.393 r_dihedral_angle_4_deg 17.907 r_dihedral_angle_3_deg 12.282 r_dihedral_angle_1_deg 6.248 r_long_range_B_refined 4.907 r_long_range_B_other 4.88 r_scangle_other 4.026 r_scbond_it 2.92 r_scbond_other 2.92 r_mcangle_it 2.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.393 r_dihedral_angle_4_deg 17.907 r_dihedral_angle_3_deg 12.282 r_dihedral_angle_1_deg 6.248 r_long_range_B_refined 4.907 r_long_range_B_other 4.88 r_scangle_other 4.026 r_scbond_it 2.92 r_scbond_other 2.92 r_mcangle_it 2.243 r_mcangle_other 2.243 r_mcbond_it 1.495 r_angle_refined_deg 1.492 r_mcbond_other 1.49 r_angle_other_deg 1.211 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6074 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XSCALE data scaling