3I6U

Structure and Activation Mechanism of the CHK2 DNA-Damage Checkpoint Kinase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GXC1GXC, 1A06
experimental modelPDB 1A061GXC, 1A06

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82951:1 ratio mix of protein solution (~12 mg/ml protein in 20 mM Tris-HCl, 150 mM NaCl, 10 mM dithiothreitol (DTT), 3% (v/v) glycerol, pH 8.0and well bifffer ( 50 mM Na2SO4 Sulfate, 14% (w/v) PEG 3350). Crystals were flash frozen in crystallization buffer supplemented with 16-20 % (v/v) glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5752.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.9α = 90
b = 152.2β = 90
c = 52.4γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 3152006-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-EAPS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
133098.30.0514.9620144

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1GXC, 1A0631217738149395.20.2470.2440.28RANDOM56.81
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]
-0.980.090.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.12
r_dihedral_angle_4_deg22.363
r_dihedral_angle_3_deg20.389
r_dihedral_angle_1_deg5.856
r_scangle_it4.301
r_mcangle_it2.914
r_scbond_it2.72
r_mcbond_it1.701
r_angle_refined_deg1.24
r_symmetry_hbond_refined0.359
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.12
r_dihedral_angle_4_deg22.363
r_dihedral_angle_3_deg20.389
r_dihedral_angle_1_deg5.856
r_scangle_it4.301
r_mcangle_it2.914
r_scbond_it2.72
r_mcbond_it1.701
r_angle_refined_deg1.24
r_symmetry_hbond_refined0.359
r_nbtor_refined0.31
r_symmetry_vdw_refined0.295
r_nbd_refined0.223
r_xyhbond_nbd_refined0.139
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6227
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement