X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AYL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH2932 ul drop containing 8 mg/ml Arg65Gln E.coli PCK, 5 mM MnCl2, 5 mM MgCl2, 2mM ATP, 2mM pyruvate, 1mM EDTA, 200 mM ammonium acetate, 100 mM sodium acetate pH 4.4 and 12% PEG 4000, was added to 2 ul drop containing 0.2 M magnesium acetate and 20% PEG 3350. Rod like crystals formed after 7 days, and where soaked in cryoprotectant solution containing 30% glycerol, 1mM EDTA, 100 mM sodium acetae, 200 mM ammonium acetate and 12% PEG 4000 for 10 seconds and flashed cooled in liquid nitrogen
Crystal Properties
Matthews coefficientSolvent content
2.3447.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.993α = 90
b = 95.301β = 96.4
c = 46.34γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105CCDRAYONIX MX300HE2013-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.98CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.9946.64691.50.353.072.13965718.69
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.920.81

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 REPLACEMENTTHROUGHOUT1AYL1.99546.0511.430873200084.020.160.15650.2105
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.285
f_angle_d0.933
f_chiral_restr0.055
f_bond_d0.007
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4135
Nucleic Acid Atoms
Solvent Atoms382
Heterogen Atoms33

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing