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Human DNA Polymerase Mu post-catalytic complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Ternary complex of human Polymerase Mu
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 Crystals were grown by mixing 1uL protein/DNA mixture with 1uL mother liquor (85-90mM HEPES pH 7.5, 17-18% PEG4000), using the sitting drop vapor diffusion technique. Crystals were transferred in two steps to a cryoprotectant solution containing 0.1M HEPES pH 7.5, 10mM MgCl2, 50mM NaCl, 20% PEG4000, 5% glycerol, 15% ethylene glycol, 10mM dTTP for 16 hours. The crystals were then backsoaked in cryoprotectant containing 2mM pyrophosphate. , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.5 50.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.018 α = 90 b = 68.67 β = 90 c = 110.444 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 93 CCD MARMOSAIC 300 mm CCD 2012-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.85 50 98.2 0.071 9.4 6.9 39012 39012 -3 22.48
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 1.85 1.88 92.1 0.442 4.1 1796
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Ternary complex of human Polymerase Mu 1.85 31.381 39012 38959 1945 98.15 0.1645 0.1626 0.1657 0.2003 0.2046 random 13.3783
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.922 f_angle_d 1.522 f_chiral_restr 0.101 f_bond_d 0.013 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2540 Nucleic Acid Atoms 364 Solvent Atoms 398 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction StructureStudio data collection HKL-2000 data reduction PHASER phasing