2XM8

Co-crystal structure of a small molecule inhibitor bound to the kinase domain of Chk2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CN5PDB ENTRY 2CN5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1 M HEPES PH 7.5, 0.2 M MAGNESIUM NITRATE, 8-16% (W/V) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.564.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.11α = 90
b = 90.11β = 90
c = 91.07γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2006-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
1339.3399.70.087.097.426154105.86
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)
13.43.5899.90.51.537.69

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENTPDB ENTRY 2CN53.429.6271.341134853299.690.26550.26280.3228
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]
-29.4313-29.431358.8625
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.956
f_angle_d0.516
f_chiral_restr0.036
f_bond_d0.002
f_plane_restr0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1843
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms23

Software

Software
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing