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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 1GXC 1GXC, 1A06 experimental model PDB 1A06 1GXC, 1A06
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 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 8.0and 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 coefficient Solvent content 2.57 52.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.9 α = 90 b = 152.2 β = 90 c = 52.4 γ = 90
Symmetry Space Group P 21 21 21
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 2006-03-03 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 30 98.3 0.051 4.96 20144
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 1GXC, 1A06 3 12 17738 1493 95.2 0.247 0.244 0.2201 0.28 RANDOM 56.81
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] -0.98 0.09 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.12 r_dihedral_angle_4_deg 22.363 r_dihedral_angle_3_deg 20.389 r_dihedral_angle_1_deg 5.856 r_scangle_it 4.301 r_mcangle_it 2.914 r_scbond_it 2.72 r_mcbond_it 1.701 r_angle_refined_deg 1.24 r_symmetry_hbond_refined 0.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.12 r_dihedral_angle_4_deg 22.363 r_dihedral_angle_3_deg 20.389 r_dihedral_angle_1_deg 5.856 r_scangle_it 4.301 r_mcangle_it 2.914 r_scbond_it 2.72 r_mcbond_it 1.701 r_angle_refined_deg 1.24 r_symmetry_hbond_refined 0.359 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.295 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.088 r_bond_refined_d 0.01 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 6227 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement