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GlnK2 from Methanothermococcus thermolithotrophicus in the apo state at a resolution of 2.3 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J9D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291.15 MtGlnK2 apo was crystallized at a concentration of 30 mg/ml in 25 mM Tris/HCl pH 7.6, 10% glycerol, 2mM dithiothreitol and 500 mM NaCl on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI).
Drop of 0.6 ul of protein was mixed with 0.6 ul of the crystallization solution. The reservoir contained 90 ul of the following crystallization solution 35 % w/v Pentaerythritol ethoxylate (15/4 EO/OH) and 100 mM HEPES pH 7.5.
Crystal Properties Matthews coefficient Solvent content 2.7 54.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.461 α = 90 b = 103.46 β = 90 c = 178.491 γ = 90
Symmetry Space Group P 2 21 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 PILATUS 2M-F 2020-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.99187 SLS X06DA
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 2.3 73.16 96.2 0.133 0.144 0.055 0.998 10.2 6.7 70360
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 2.3 2.4 81.3 1.151 1.259 0.508 0.671 1.5 6
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 2J9D 2.3 73.16 85.43 70326 3625 82.04 0.233 0.2215 0.2176 0.2445 0.2397 37.6095
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 9066 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction autoPROC data reduction autoPROC data scaling MOLREP phasing