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Nucleotidyl Transfer Mechanism of Mismatched dNTP Incorporation by DNA Polymerase b by Structural and Kinetic Analyses
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BPD PDB ENTRY 1BPD
Crystallization Crystal Properties Matthews coefficient Solvent content 2.43 48.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.862 α = 90 b = 119.43 β = 90 c = 38.013 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU IMAGE PLATE M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 2.1 20 98 0.04 27.8 3 16773 2 16.1
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 20 89.8 0.16 6.4
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1BPD 2.1 19.91 15738 806 96.6 0.217 0.217 0.2163 0.249 0.2483 RANDOM 28.7
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] -5.03 -9.01 14.04
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_scangle_it 3.35 c_scbond_it 2.21 c_mcangle_it 2.1 c_mcbond_it 1.39 c_angle_deg 1.2 c_improper_angle_d 0.75 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_scangle_it 3.35 c_scbond_it 2.21 c_mcangle_it 2.1 c_mcbond_it 1.39 c_angle_deg 1.2 c_improper_angle_d 0.75 c_bond_d 0.005 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 1953 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing