3GIG

Crystal structure of phosphorylated DesKC in complex with AMP-PCP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EHG3EHG and 3EHF
experimental modelPDB 3EHF3EHG and 3EHF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.5291PEG3000, MgCl2, CHES, AMP-PCP, pH 9.5, vapor diffusion, hanging drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
4.270.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.63α = 90
b = 94.63β = 90
c = 162.46γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2008-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
13.528.84699.20.0473.81105110993-3-392.42
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)
3.53.699.30.31943.9864

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3EHG and 3EHF3.50228.8461.991099089699.450.2910.2870.335random147.188
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]
-18.125-18.125-24.158
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d25.66
f_angle_d2.718
f_chiral_restr0.167
f_bond_d0.027
f_plane_restr0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2967
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms64

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction