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Structure of Helicobacter pylori EgtU bound to EGT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8DP6 PDB entry 8DP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2 M ammonium sulfate, 0.1 M sodium acetate, 22% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.8 56.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.716 α = 90 b = 137.751 β = 90 c = 190.496 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 80 PIXEL DECTRIS EIGER X 16M 2021-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.35 39.54 99.9 0.42 0.854 4.3 6.9 25843 102.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.35 39.54 99.9 3.422 0.119 1
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 8DP6 3.35 39.54 1.33 24325 1978 94.09 0.231 0.2281 0.288 0.2878 97.65
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10855 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 75
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing