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WT human DNA polymerase beta, Ternary complex dT:dAmpCpp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FMS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
Crystal Properties Matthews coefficient Solvent content 2.22 44.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.616 α = 90 b = 79.032 β = 107.39 c = 55.556 γ = 90
Symmetry Space Group P 1 21 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 Bruker PHOTON II 2025-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS MICROFOCUS 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.93 24.97 99.74 0.074 0.087 0.044 0.997 13.6 3.73 60098 17.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2 98.42 0.469 0.579 0.334 0.72 2.6 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.93 24.97 1.34 60098 5950 97.33 0.1596 0.1551 0.153 0.2011 0.2011
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 19.702 f_angle_d 0.889 f_chiral_restr 0.049 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2612 Nucleic Acid Atoms 630 Solvent Atoms 502 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement PROTEUM PLUS data scaling PROTEUM PLUS data reduction PDB_EXTRACT data extraction PHENIX phasing