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Structure of a mutant of the large fragment of DNA polymerase I from Thermus Auqaticus in complex with an abasic site and ddATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LWL PDB entry 3LWL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.8 291 0.05M Tris HCl, 0.2M NH4Cl, 0.01M CaCl2, 28% PEG 4000, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.28 45.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.301 α = 90 b = 109.301 β = 90 c = 90.318 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M Dynamically bendable mirror, LN2 cooled fixed-exit, Si(111) monochromator 2010-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 SLS X06SA
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 2.3 50 99.5 0.145 12.82 9.04 24927 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.43 1.24 5.61
Refinement Statistics Diffraction ID Structure Solution 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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 3LWL 2.39 47.33 1.99 24927 24927 1287 99.7 0.212 0.21 0.2074 0.266 0.2644
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] 2.8507 2.8507 -11.6363
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.508 f_angle_d 0.921 f_chiral_restr 0.048 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4197 Nucleic Acid Atoms 499 Solvent Atoms 131 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX model building PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing