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DNA Polymerase Lambda I493K E529D, TMP:At Ca2+ Ground State Ternary Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7M43
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277.15 20 mM bicine pH7.5
300 mM Na-K tartrate
20% PEG 20K
Crystal Properties Matthews coefficient Solvent content 2.91 57.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.4 α = 90 b = 62.47 β = 90 c = 139.57 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 PIXEL DECTRIS EIGER X 9M 2023-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.12 46.55 99.8 0.038 0.99 16.6 13.4 28562
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.18 0.69 0.794 1.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.12 35.89 1.34 28539 1426 99.76 0.2037 0.2015 0.1994 0.2449 0.2423 RANDOM 51.42
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 20.1429 f_angle_d 0.925 f_chiral_restr 0.0523 f_plane_restr 0.0094 f_bond_d 0.0081
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2465 Nucleic Acid Atoms 426 Solvent Atoms 210 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing