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MBD2 in complex with double-stranded DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other rigid body refinement (refmac5/dimple) of a currently unpublished, isomorphous structure of a similar MBD2-DNA complex against current data.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 25% PEG-3350, 0.1 M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.9 57.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.013 α = 84.5 b = 40.198 β = 85.48 c = 105.158 γ = 62.71
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 PILATUS3 6M 2017-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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 35.64 94.8 0.04 0.054 0.037 0.998 10 1.9 34483
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 2.05 81.4 0.76 1.032 0.694 0.465 1.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT rigid body refinement (refmac5/dimple) of a currently unpublished, isomorphous structure of a similar MBD2-DNA complex against current data. 2.3 34.8 22079 821 96.09 0.234 0.2327 0.2677 0.2752 49.143
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] -1.7 -0.48 0.31 0.58 0.04 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.659 r_dihedral_angle_4_deg 20.108 r_dihedral_angle_3_deg 14.439 r_dihedral_angle_1_deg 6.78 r_mcangle_it 2.161 r_angle_refined_deg 1.786 r_mcbond_it 1.365 r_mcbond_other 1.357 r_angle_other_deg 1.23 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.659 r_dihedral_angle_4_deg 20.108 r_dihedral_angle_3_deg 14.439 r_dihedral_angle_1_deg 6.78 r_mcangle_it 2.161 r_angle_refined_deg 1.786 r_mcbond_it 1.365 r_mcbond_other 1.357 r_angle_other_deg 1.23 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2024 Nucleic Acid Atoms 972 Solvent Atoms 29 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing