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Crystal structure of Methanobrevibacter smithii Dph2 in complex with Methanobrevibacter smithii elongation factor 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H7J Methanobrevibacter smithii Dph2, Pyrococcus horikoshii EF-2 (5H7J)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 290 The reservoir solution contained 100 mM Tris, pH 7.2, 200 mM MgSO4, and 21 % (w/v) PEG400; NaCl was added to the reservoir to a final concentration of 300 mM after forming the drop
Crystal Properties Matthews coefficient Solvent content 2.93 58.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.899 α = 90 b = 322.979 β = 90 c = 172.432 γ = 90
Symmetry Space Group C 2 2 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 EIGER X 16M 2018-07-05 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) R Merge I (Observed) 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 3.45 49.4 99.7 0.075 0.998 8.7 4.1 37395
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.45 3.64 0.568
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 Methanobrevibacter smithii Dph2, Pyrococcus horikoshii EF-2 (5H7J) 3.45 49.356 1.33 37270 1864 99.33 0.226 0.2238 0.2266 0.2665 0.2647 208.7438
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 12169 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing