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Crystal structure of Salmonella typhimurium FabG in complex with NADPH at 1.5 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AFN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M LiSO4
0.1 M HEPES pH 7.5
25 %w/v PEG3350
10 mM NADPH (added to the protein solution)
Cryoprotection of the crystals: dipping them in
0.2 M LiSO4
0.1 M HEPES pH 7.5
25 %w/v PEG3350
26% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.18 43.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.43 α = 90 b = 71.144 β = 94.42 c = 81.366 γ = 90
Symmetry Space Group I 1 2 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 PIXEL DECTRIS PILATUS3 S 6M toroidal mirror 2016-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97625 ESRF ID23-1
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 1.5 58.49 95.9 0.025 0.032 0.02 0.999 18.3 2.3 67342 2.5
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 1.5 1.53 97.4 0.387 0.491 0.335 0.843 2.5 2.3
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 4AFN 1.5 58.21 63956 3434 95.69 0.1602 0.1588 0.1598 0.185 0.1645 RANDOM 25.223
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] 0.39 -0.34 1.15 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.263 r_dihedral_angle_4_deg 14.5 r_dihedral_angle_3_deg 13.385 r_dihedral_angle_1_deg 5.612 r_angle_refined_deg 1.479 r_angle_other_deg 0.934 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.263 r_dihedral_angle_4_deg 14.5 r_dihedral_angle_3_deg 13.385 r_dihedral_angle_1_deg 5.612 r_angle_refined_deg 1.479 r_angle_other_deg 0.934 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3554 Nucleic Acid Atoms Solvent Atoms 456 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing