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Crystal structure of dehydrogenase/isomerase FabX from Helicobacter pylori in complex with inhibitor 1872
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7E1Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Tris-HCl, pH 7.0, 25% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.13 42.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.175 α = 90 b = 48.505 β = 93.79 c = 75.897 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2023-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 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 1.6 41.22 92.6 0.062 0.068 0.028 0.999 16.4 5.9 41739
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 1.6 1.69 72.3 0.417 0.479 0.226 0.865 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 30.32 1.34 41270 2168 91.6 0.2202 0.2186 0.2191 0.2483 0.2494
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 10.462 f_angle_d 1.082 f_chiral_restr 0.072 f_plane_restr 0.009 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2724 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 67
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing