7P52

GlnK1 from Methanocaldococcus jannaschii with Mg-ATP and 2-oxoglutarate at a resolution of 1.2 A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5291.15GlnK1 was crystallized at 11.2 mg/ml in 25 mM Tris/HCl pH 7.6, 10% glycerol, 2mM dithiothreitol and 500mM NaCl on 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). GlnK1 was cocrystallized with 2 mM ATP, 2 mM 2-oxoglutarate and 2 mM MgCl2. 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: 20% PEG 3,350, 100 mM Bis-Tris propane pH 8.5 and 200 mM sodium nitrate.
Crystal Properties
Matthews coefficientSolvent content
358.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.053α = 90
b = 89.053β = 90
c = 98.059γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2020-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.99187SLSX06DA

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
11.244.526589.80.0570.060.020.99917.89.431673
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)
11.21.2499.61.2091.290.4430.6421.78.3

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 REPLACEMENTTHROUGHOUT2J9D1.2000244.52651.3531668155067.740.13240.13110.155421.9875
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 Atoms878
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms52

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing