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Structure and Activation Mechanism of the CHK2 DNA-Damage Checkpoint Kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I6U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 1:1 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 8.0 and well bufffer (100 mM NaHepes, 300 mM Ammonium Tartrate, 22% PEG 3350, pH 7.0). Crystals were flash frozen in
crystallization buffer supplemented with 16-20% (v/v) glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.57 52.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.2 α = 84.1 b = 114.7 β = 81.2 c = 123 γ = 80.7
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315 2006-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.25 30 96.2 0.042 1.8 60983
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3I6U 3.25 30 56117 1755 90.8 0.252 0.251 0.24 0.287 RANDOM 137.5
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] -0.26 -0.34 1.73 -3.09 -3.45 3.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.202 r_dihedral_angle_4_deg 21.623 r_dihedral_angle_3_deg 19.937 r_dihedral_angle_1_deg 5.446 r_scangle_it 4.357 r_scbond_it 2.596 r_mcangle_it 2.574 r_mcbond_it 1.442 r_angle_refined_deg 1.138 r_symmetry_hbond_refined 0.626
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.202 r_dihedral_angle_4_deg 21.623 r_dihedral_angle_3_deg 19.937 r_dihedral_angle_1_deg 5.446 r_scangle_it 4.357 r_scbond_it 2.596 r_mcangle_it 2.574 r_mcbond_it 1.442 r_angle_refined_deg 1.138 r_symmetry_hbond_refined 0.626 r_symmetry_vdw_refined 0.619 r_nbtor_refined 0.31 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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 Atoms Number Protein Atoms 24560 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement