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Homeobox transcription factor CDX1 bound to methylated DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LTX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 PEG MME (5000),KCl, MgCl2, 2-Methyl propanol, Tris buffer
Crystal Properties Matthews coefficient Solvent content 2.3 46.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.65 α = 90 b = 45.555 β = 93.79 c = 116.499 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 2016-07-03 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) 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 3.23 58.12 97.2 0.174 0.995 5.3 3.4 5425 57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.23 3.49 88.9 0.533 0.891 1.91 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 5LTX 3.23 58.12 4909 515 97.12 0.2467 0.2411 0.2399 0.2995 0.2948 RANDOM 90.603
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] 4.69 0.38 -2.68 -2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.059 r_dihedral_angle_3_deg 21.348 r_dihedral_angle_4_deg 15.538 r_dihedral_angle_1_deg 8.182 r_mcangle_it 6.051 r_mcbond_it 3.548 r_mcbond_other 3.529 r_angle_refined_deg 1.852 r_angle_other_deg 1.689 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.059 r_dihedral_angle_3_deg 21.348 r_dihedral_angle_4_deg 15.538 r_dihedral_angle_1_deg 8.182 r_mcangle_it 6.051 r_mcbond_it 3.548 r_mcbond_other 3.529 r_angle_refined_deg 1.852 r_angle_other_deg 1.689 r_chiral_restr 0.124 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1103 Nucleic Acid Atoms 1439 Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing