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The crystal structure of Pol2CORE in complex with DNA and an incoming nucleotide, carrying an Fe-S cluster
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M8O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 10mM Tris HCl pH8, 10mM CaCl2, 15% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.87 57.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.36 α = 90 b = 70.402 β = 112.99 c = 154.24 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 EIGER X 4M 2018-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.96770 ESRF MASSIF-3
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 2.8 78.48 98.5 0.126 0.143 0.066 0.995 7.8 4.3 38251
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 2.8 2.92 99.2 1.082 1.224 0.561 0.447 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 4m8o 2.8 78.48 36257 1868 98.35 0.2265 0.2234 0.2277 0.2856 0.2856 RANDOM 69.068
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] 18.51 -6.78 24.36 -42.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.985 r_dihedral_angle_3_deg 19.209 r_dihedral_angle_4_deg 17.039 r_dihedral_angle_1_deg 7.009 r_angle_refined_deg 1.057 r_chiral_restr 0.096 r_gen_planes_refined 0.004 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8608 Nucleic Acid Atoms 529 Solvent Atoms Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PDB_EXTRACT data extraction Coot model building PHASER phasing