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Complex of MBD1-MBD and methylated DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CC8 earlier version of PDB entry 6cc8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 30% PEG-550-MME, 0.1 M magnesium chloride, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.5 49.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.574 α = 90 b = 74.193 β = 90 c = 138.872 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2012-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97911 APS 19-ID
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 2.25 46.29 99.9 0.056 0.061 0.023 0.999 20.3 6.9 7412
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 2.25 2.32 100 1.083 1.167 0.43 0.641 7.2 674
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT earlier version of PDB entry 6cc8 2.25 37.1 6633 748 99.81 0.2382 0.2349 0.241 0.2693 0.2751 51.071
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] 0.5 -0.77 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 26.124 r_dihedral_angle_2_deg 17.132 r_dihedral_angle_3_deg 16.784 r_dihedral_angle_1_deg 6.121 r_mcangle_it 2.294 r_angle_refined_deg 1.533 r_mcbond_it 1.416 r_mcbond_other 1.414 r_angle_other_deg 0.991 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 26.124 r_dihedral_angle_2_deg 17.132 r_dihedral_angle_3_deg 16.784 r_dihedral_angle_1_deg 6.121 r_mcangle_it 2.294 r_angle_refined_deg 1.533 r_mcbond_it 1.416 r_mcbond_other 1.414 r_angle_other_deg 0.991 r_chiral_restr 0.075 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 527 Nucleic Acid Atoms 488 Solvent Atoms Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing