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Structure of CDX2-DNA(TCG)
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 19% PME 5000, 0.15 M potassium chloride, 0.1 M magnesium chloride, 8% PEG 400, 0.05M TRIS-buffer pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.35 47.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.95 α = 90 b = 46.49 β = 113.27 c = 68.89 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 PILATUS 6M-F 2017-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9724 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.18 43.23 99.6 0.185 0.191 0.998 8.47 16.093 19575 -3 65.834
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.24 97.8 2.991 3.273 0.107 0.43 6.019
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 2.57 43.23 10891 1210 99.95 0.2221 0.2161 0.2184 0.2781 0.2782 RANDOM 67.057
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] 7.15 2.1 -8.04 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.432 r_dihedral_angle_3_deg 21.448 r_dihedral_angle_1_deg 19.438 r_dihedral_angle_4_deg 11.958 r_angle_refined_deg 2.053 r_angle_other_deg 1.558 r_chiral_restr 0.183 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.432 r_dihedral_angle_3_deg 21.448 r_dihedral_angle_1_deg 19.438 r_dihedral_angle_4_deg 11.958 r_angle_refined_deg 2.053 r_angle_other_deg 1.558 r_chiral_restr 0.183 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1272 Nucleic Acid Atoms 1476 Solvent Atoms 93 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing