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Structure of the E.coli DNA polymerase sliding clamp with a covalently bound peptide 3.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FVL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293.15 0.2 M Potassium nitrate
20% PEG 3350, pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.76 55.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.84 α = 90 b = 66.57 β = 129.03 c = 80.98 γ = 90
Symmetry Space Group C 1 2 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 DECTRIS PILATUS 2M-F 2020-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.37 54.81 91.5 0.99 16.7 6.8 79966 1.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.37 1.45 0.49
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 1.45 54.81 1.37 75874 1892 94.5 0.158 0.1571 0.1607 0.1953 0.1957
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 11.036 f_angle_d 1.415 f_chiral_restr 0.119 f_plane_restr 0.016 f_bond_d 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2919 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling autoPROC data processing XDS data reduction MOLREP phasing