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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 7 291 20% PEG-3350, 50 mM Hepes-NaOH pH 7.0, 10 mM MgCl2, 400 mM LiAc, and 10 mM 2-aminoethanesulfonic acid (taurine) 2 VAPOR DIFFUSION, HANGING DROP 7 291 20% PEG-3350, 50 mM Hepes-NaOH pH 7.0, 10 mM MgCl2, 400 mM LiAc, and 10 mM 2-aminoethanesulfonic acid (taurine)
Crystal Properties Matthews coefficient Solvent content 2.53 51.35 2.53 51.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.21 α = 90 b = 70.04 β = 109.43 c = 149.93 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 90 PIXEL DECTRIS PILATUS3 6M 2017-07-13 M SINGLE WAVELENGTH 2 1 x-ray 90 PIXEL DECTRIS PILATUS3 6M 2017-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.98400 ESRF ID23-1 2 SYNCHROTRON ESRF BEAMLINE ID23-1 1.73598 ESRF ID23-1
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 2.7 73.04 98.6 0.152 0.186 0.106 0.972 5.1 2.9 39543 57.09
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 2.7 2.81 97.5 1.654 2.046 1.188 0.144 2.7
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 THROUGHOUT 4m8o 2.7 19.99 1.33 39250 1956 97.96 0.24 0.2386 0.2437 0.2659 0.2669 64.9752
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8428 Nucleic Acid Atoms 529 Solvent Atoms 6 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing