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Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DQQ PDB ENTRY 4DQQ chains A, B, and C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 290 47% Saturated Ammonium Sulfate, 2.5% MPD, 10mM MgSO4, 100mM MES (pH 5.8), VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.91 57.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.86 α = 90 b = 93.78 β = 90 c = 104.87 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 CCD ADSC QUANTUM 315 2011-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.1159 ALS 12.3.1
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 1.58 100 98.8 0.059 24.7 10 117529 -3 26.883
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 1.58 1.67 98.9 0.476 4.33
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 4DQQ chains A, B, and C 1.58 54.703 2.35 112902 5646 94.93 0.1621 0.1611 0.1812 0.1827
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] 5.1404 -1.9461 -3.1943
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.655 f_angle_d 1.335 f_chiral_restr 0.07 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4639 Nucleic Acid Atoms 365 Solvent Atoms 824 Heterogen Atoms 89
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing