7P50

GlnK2 from Methanothermococcus thermolithotrophicus in complex with Mg-ATP and 2-oxoglutarate at a resolution of 1.16 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J9D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5291.15MtGlnK2 was crystallized at a concentration of 30 mg/ml in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 2 mM dithiothreitol and 500 mM NaCl. The protein was co-crystallized with 2 mM ATP, 2 mM 2-oxoglutarate and 2 mM MgCl2 on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). Drop of 0.6 ul of protein sample was mixed with 0.6 ul of the crystallization solution. The reservoir contained 90 ul of the following crystallization solution: 25 w/v Pentaerythritol ethoxylate (3/4 EO/OH), 100 mM MES pH 6.5.
Crystal Properties
Matthews coefficientSolvent content
2.244.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.238α = 90
b = 58.238β = 90
c = 229.304γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.99985SLSX06DA

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.15757.3393.20.0490.050.010.99929.121.6108153
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)RedundancyNumber Unique Reflections (All)
11.1571.25951.70.6430.7090.2860.7741.75.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2J9D1.1657.331.35108153530977.80.11780.11680.136620.8654
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 AtomsNumber
Protein Atoms2748
Nucleic Acid Atoms
Solvent Atoms516
Heterogen Atoms145

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing