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Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BDP PDB ENTRY 2BDP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 290 AMMONIUM SULFATE, MAGNESIUM SULFATE, MPD, MES, MANGANESE SULFATE, pH 5.80, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K
Crystal Properties Matthews coefficient Solvent content 3.12 60.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.681 α = 90 b = 91.681 β = 90 c = 190.116 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 MIRROR 2001-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 1.95 39.7 99.8 0.062 18.6 4.9 129531 129531 -3 23.2
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) 1.95 2.02 99.3 0.48 2.5 4.1 12800
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2BDP 1.95 39.7 2 98839 96536 4574 74.2 0.264 0.218 0.218 0.2295 0.261 0.2716 RANDOM 43.9
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] 0.3 0.74 0.3 -0.6
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_improper_angle_d 1.42 c_angle_deg 1.3 c_scangle_it 1.26 c_mcangle_it 1.12 c_scbond_it 0.83 c_mcbond_it 0.66 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9294 Nucleic Acid Atoms 974 Solvent Atoms 186 Heterogen Atoms 69
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing