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Crystal structure of family B DNA polymerase from hyperthermophilic archaeon pyrococcus kodakaraensis KOD1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 MPD, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.51 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.64 α = 90 b = 111.38 β = 90 c = 111.93 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 100 DIFFRACTOMETER WEISSENBERG 1999-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B Photon Factory BL-18B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.8 40 88.1 0.084 8.7 20298 1 20.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 83.7 0.345
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3 35.24 16749 1631 89.2 0.231 0.231 0.2086 0.313 0.2917 RANDOM 55.7
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] 24.2 1.85 -26.05
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.3 c_scangle_it 2.61 c_mcangle_it 2.27 c_scbond_it 1.62 c_mcbond_it 1.29 c_angle_deg 1.1 c_improper_angle_d 0.74 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.3 c_scangle_it 2.61 c_mcangle_it 2.27 c_scbond_it 1.62 c_mcbond_it 1.29 c_angle_deg 1.1 c_improper_angle_d 0.74 c_bond_d 0.007 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 5703 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose CNS refinement