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Crystal structure of 3-oxoacyl-ACP reductase FabG in complex with NADP+ and 3-keto-octanoyl-ACP from Helicobacter pylori in an inactive form that priors the acyl substrate delivery
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JFG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M Imidazole pH 7.0, 30% v/v MPD
Crystal Properties Matthews coefficient Solvent content 2.2 44.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.942 α = 90 b = 117.259 β = 90 c = 142.258 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 PILATUS3 6M 2022-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9875 SSRF BL19U1
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 50 100 0.176 0.184 0.051 0.989 4.3 12.1 106064
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 1.86 99.9 0.624 0.662 0.219 0.866 8.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 8JFG 1.8 45.24 1.35 105645 5273 99.4 0.165 0.164 0.1658 0.19 0.1928
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.92 f_angle_d 1.287 f_chiral_restr 0.094 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8376 Nucleic Acid Atoms Solvent Atoms 1163 Heterogen Atoms 125
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing