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Structure of CDX2-DNA(CAA)
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 27 % PME 5000, 0.15M potassium chloride, 0.1M magnesium chloride, 8% PEG 400, 0.05M TRIS buffer
Crystal Properties Matthews coefficient Solvent content 2.61 52.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.248 α = 90 b = 46.695 β = 101.4 c = 128.634 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 2016-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972420 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 2.95 66.19 96.6 0.077 0.093 0.051 0.998 7.5 3.2 8494
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 2.95 3.13 90.5 0.83 0.993 0.539 0.611 3.2
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 2.95 66.19 8076 418 96.49 0.2103 0.2085 0.2088 0.2439 0.2364 RANDOM 98.684
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] 0.64 -3.27 0.01 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.217 r_dihedral_angle_3_deg 24.915 r_dihedral_angle_4_deg 14.084 r_dihedral_angle_1_deg 5.898 r_angle_refined_deg 1.918 r_angle_other_deg 1.488 r_chiral_restr 0.118 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.217 r_dihedral_angle_3_deg 24.915 r_dihedral_angle_4_deg 14.084 r_dihedral_angle_1_deg 5.898 r_angle_refined_deg 1.918 r_angle_other_deg 1.488 r_chiral_restr 0.118 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1236 Nucleic Acid Atoms 1476 Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing