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MBD2 in complex with a deoxy-oligonucleotide
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Type Source Accession Code Details experimental model Other rigid body refinement (refmac5/dimple) of a currently unpublished, isomorphous structure of a similar MBD2-DNA complex against current data.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 291 20% PEG-3350, 0.2 M potassium dihydrogen phosphate
Crystal Properties Matthews coefficient Solvent content 2.8 56.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.912 α = 84.48 b = 40.015 β = 85.91 c = 105.89 γ = 62.77
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 0.97934 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 1.99 35.49 92.6 0.036 0.049 0.033 0.998 11.3 1.9 33843
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 1.99 2.05 63 0.578 0.786 0.53 0.588 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT rigid body refinement (refmac5/dimple) of a currently unpublished, isomorphous structure of a similar MBD2-DNA complex against current data. 2.3 35.1 21914 808 95.39 0.2331 0.2316 0.2431 0.2717 0.2778 thin resolution shells (sftools) 48.293
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] -0.53 -0.83 0.98 0.87 -0.78 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.992 r_dihedral_angle_4_deg 18.842 r_dihedral_angle_3_deg 14.053 r_dihedral_angle_1_deg 6.669 r_mcangle_it 2.17 r_angle_refined_deg 1.793 r_mcbond_it 1.353 r_mcbond_other 1.352 r_angle_other_deg 1.219 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.992 r_dihedral_angle_4_deg 18.842 r_dihedral_angle_3_deg 14.053 r_dihedral_angle_1_deg 6.669 r_mcangle_it 2.17 r_angle_refined_deg 1.793 r_mcbond_it 1.353 r_mcbond_other 1.352 r_angle_other_deg 1.219 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2035 Nucleic Acid Atoms 974 Solvent Atoms 25 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing