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Crystal structure of TET2-DNA in complex with IOX1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NE3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 24 % PEG 2000MME, 100 mM MES pH 7.0
25 mg/mL protein 1:1 with DNA plus 5 mM IOX1
Seeding experiment (1 ul reservoir + 1 ul protein:DNA:IOX1 + 0.2 ul seeding solution)
Crystal Properties Matthews coefficient Solvent content 2.37 48.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.44 α = 90 b = 89.13 β = 90 c = 268.25 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 X 9M 2024-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873128 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.9 50 98.3 0.106 0.999 17.08 13.43 45640 31.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 93.2 1.141 0.526 2.74 12.43
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 1.9 42.56 1.36 45635 2281 98.31 0.1912 0.1896 0.19 0.2206 0.2205 46
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 17.4601 f_angle_d 0.6322 f_chiral_restr 0.0435 f_plane_restr 0.0043 f_bond_d 0.0033
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3109 Nucleic Acid Atoms 494 Solvent Atoms 235 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing