7P4V

GlnK1 from Methanothermococcus thermolithotrophicus with dADP at a resolution of 1.94 A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5291.15GlnK1 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 coefficientSolvent content
3.4864.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.296α = 90
b = 87.296β = 90
c = 46.01γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2019-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00003SLSX06DA

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
11.9475.60189.10.0530.0550.0130.99927.319.310108
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)
11.942.14860.21.7111.7590.4030.7731.818.6

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 REPLACEMENTTHROUGHOUT2J9D1.9439.31.34999549265.540.1980.19660.225762.7293
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 AtomsNumber
Protein Atoms882
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms28

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing