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transcription factor CDX2 bound to hydroxymethylated DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 PEG 1500, potassium chloride, magnesium chloride, PEG 200, Bis-tris propane, 8.0
Crystal Properties Matthews coefficient Solvent content 2.16 49.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.897 α = 90 b = 46.634 β = 98.25 c = 120.048 γ = 90
Symmetry Space Group I 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 6M-F 2018-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 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 3.03 43.45 97 0.272 0.315 0.155 0.975 4.5 3.8 7406
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 3.03 3.21 89.3 1.409 1.623 0.788 0.745 3.7
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 5LTY 3.2 43.45 6054 341 98.16 0.24 0.2378 0.2379 0.2794 0.2751 RANDOM 70.605
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] 3.88 -1.71 -6.2 2.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 29.339 r_dihedral_angle_2_deg 28.499 r_dihedral_angle_4_deg 16.855 r_dihedral_angle_1_deg 5.738 r_angle_refined_deg 2.264 r_angle_other_deg 1.062 r_chiral_restr 0.138 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 29.339 r_dihedral_angle_2_deg 28.499 r_dihedral_angle_4_deg 16.855 r_dihedral_angle_1_deg 5.738 r_angle_refined_deg 2.264 r_angle_other_deg 1.062 r_chiral_restr 0.138 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1138 Nucleic Acid Atoms 1484 Solvent Atoms 14 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing