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ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 19mer DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other used previous structures for ZF3-7 with DNA and single ZF search for ZF8-10
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 0.04 M Citric acid,
0.06 M BIS-TRIS propane/pH 6.4,
20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 3.4 63.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.464 α = 90 b = 80.464 β = 90 c = 187.598 γ = 120
Symmetry Space Group P 32 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 16M 2020-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00000 APS 22-ID
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 2.89 39.34 99.9 0.065 0.974 12.8 10.3 30234 78.7
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 2.89 2.99 0.86 0.706 1.5 9.7
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 2.89 39.34 1.34 29628 1460 97.59 0.2018 0.1998 0.2014 0.2403 0.2399 93.66
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 21.8318 f_angle_d 0.5029 f_chiral_restr 0.0347 f_bond_d 0.0031 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1885 Nucleic Acid Atoms 772 Solvent Atoms 6 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement SERGUI data collection HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing