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ThDP-Mn2+ complex of R413K variant of EcMenD soaked with 2-ketoglutarate for 5 min
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EJ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.14M Magnesium formate, 12% PEG 3350, 0.1M HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.41 48.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.26 α = 83.43 b = 90.27 β = 76.14 c = 167.07 γ = 63.49
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 2017-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.979 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 20.64 78.1 0.081 7 2.2 159070
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 77.2 0.127 2
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 THROUGHOUT 5EJ8 2.3 20.64 1.97 159058 2015 78.2 0.166 0.165 0.1673 0.207 0.203 16.72
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 34123 Nucleic Acid Atoms Solvent Atoms 2516 Heterogen Atoms 352
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction Aimless data scaling PHENIX phasing