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Crystal structure of enoyl-ACP reductase FabI in complex with NAD+ and crotonyl-ACP from Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M sodium citrate pH 5.5, 15% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 3.22 61.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.272 α = 90 b = 101.816 β = 90 c = 126.329 γ = 90
Symmetry Space Group I 2 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 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 2.4 50 99.4 0.172 0.18 0.051 0.979 6.2 12.1 19566
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 2.4 2.49 93.8 0.906 0.961 0.311 0.898 7.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 8JFM 2.41 40.29 1.34 16395 803 83.3 0.1858 0.1833 0.2353 0.2501
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 21.36 f_angle_d 1.119 f_chiral_restr 0.057 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2707 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing