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GlnK1 from Methanothermococcus thermolithotrophicus with dADP at a resolution of 1.94 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 6.5 291.15 GlnK1 crystallized at a concentration of 33 mg/ml in 25 mM TrisHCl pH 7.6, 10% glycerol, 2mM dithiothreitol and 500mM NaCl . Drop of 0.6 ul of protein was mixed with 0.6 ul of the crystallization solution in a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). The reservoir contained 90 ul of the following crystallization solution: 35 % w/v Pentaerythritol propoxylate (17/8 PO/OH), 100 mM MES pH 6.5, 200 mM Ammonium sulfate.
Crystal Properties Matthews coefficient Solvent content 3.48 64.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.296 α = 90 b = 87.296 β = 90 c = 46.01 γ = 120
Symmetry Space Group P 3 2 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 2M-F 2019-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00003 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 1.94 75.601 89.1 0.053 0.055 0.013 0.999 27.3 19.3 10108
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 1.94 2.148 60.2 1.711 1.759 0.403 0.773 1.8 18.6
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 1.94 39.3 1.34 9995 492 65.54 0.198 0.1966 0.1981 0.2257 0.2219 62.7293
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 882 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction autoPROC data reduction autoPROC data scaling MOLREP phasing