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Crystal structure of the catalytic core of human DNA polymerase kappa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.75 293 8% PEG 8K, 8% Ethylene Glycol, and 100mM HEPES (pH 7.75), VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal Properties Matthews coefficient Solvent content 2.485 50.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.209 α = 90 b = 109.46 β = 90 c = 111.205 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 110 CCD ADSC QUANTUM 4 Diamond (111) double-crystal monochromator 2003-06-13 M SINGLE WAVELENGTH 2 1 x-ray CCD SBC-2 Bent cylindrical Si-mirror (Rh coating) 2003-06-30 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.12709 APS 14-ID-B 2 SYNCHROTRON APS BEAMLINE 19-ID 0.97934, 0.97920, 0.96859 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1,2 2.4 50 0.064 0.064 11 76925 -3 -3 23.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.49 99.4 0.436 0.019 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.4 20.03 78579 71651 3529 91.2 0.246 0.246 0.282 RANDOM 40.4
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] -8.97 5.15 3.82
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_scangle_it 2.89 c_mcangle_it 2.24 c_scbond_it 1.91 c_angle_deg 1.7 c_mcbond_it 1.31 c_improper_angle_d 1.13 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_scangle_it 2.89 c_mcangle_it 2.24 c_scbond_it 1.91 c_angle_deg 1.7 c_mcbond_it 1.31 c_improper_angle_d 1.13 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6172 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling SOLVE phasing CNS refinement HKL-2000 data reduction