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Crystal structure of E. coli FabI bound to the thiocarbamoylated benzodiazaborine inhibitor 35b.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CFZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.1M citrate pH 7.0, 0.1M ammonium sulfate, 22%w/v PEG 2000
Crystal Properties Matthews coefficient Solvent content 2.28 46.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.913 α = 90 b = 79.913 β = 90 c = 323.789 γ = 120
Symmetry Space Group P 61 2 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 PILATUS 6M 2014-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97950 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.11 69.21 99.3 0.048 0.049 0.012 42.6 17.2 36240 36240
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.23 95 0.115 0.115 0.03 6.3 14 4921
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 5CFZ 2.11 69.21 34171 1836 98.79 0.2039 0.2019 0.1974 0.2413 0.2344 RANDOM 24.417
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] 0.02 0.01 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.236 r_dihedral_angle_4_deg 16.409 r_dihedral_angle_3_deg 13.574 r_dihedral_angle_1_deg 6.442 r_angle_refined_deg 1.492 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3510 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing