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Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing undamaged template dG and bound incoming CMPCPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M04
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 82mM HEPES pH 7.5, 82mM NaCl, 8.2% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.84 56.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.802 α = 90 b = 68.692 β = 90 c = 110.065 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 100 CCD RIGAKU SATURN 944 VARIMAX HF 2017-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.75 50 99.9 0.056 0.059 0.017 34.4 10.1 46387
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 97.9 0.404 0.456 0.207 0.871 3.13 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4M04 1.751 29.901 1.34 46317 2320 99.79 0.1645 0.1632 0.1655 0.1899 0.1929 random
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 9.836 f_angle_d 1.076 f_chiral_restr 0.059 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2553 Nucleic Acid Atoms 345 Solvent Atoms 388 Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing