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DNA Polymerase Mu Product Complex, Mn2+ (960 min)
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 7.5 277 85-90mM HEPES pH 7.5, 17-18% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.67 53.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.934 α = 90 b = 68.653 β = 90 c = 109.999 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 2015-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 1.98 50 99.4 0.095 8.5 8.5 32271 23.77
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 1.98 2.01 94 0.69 4.7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4M04 1.977 21.982 1.33 31980 1598 98.61 0.1774 0.1755 0.1806 0.2149 0.2183 36.3937
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 13.51 f_angle_d 0.68 f_chiral_restr 0.044 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2551 Nucleic Acid Atoms 364 Solvent Atoms 325 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing