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Crystal structure MBD3 MBD domain in complex with methylated CpG DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C2K PDB ENTRY 6C2K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.8 55.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.55 α = 90 b = 36.64 β = 92.77 c = 130.93 γ = 90
Symmetry Space Group C 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 CCD ADSC QUANTUM 315r 2012-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97923 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 35.73 99.9 0.074 14 5.3 25160
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 99.8 0.761 3.7
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 6C2K 1.95 35.73 23724 1436 99.8 0.226 0.224 0.2337 0.259 0.2582 THIN RESOLUTION SHELLS
(SFTOOLS) 42.99
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] -0.54 0.06 0.8 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.405 r_dihedral_angle_4_deg 17.33 r_dihedral_angle_3_deg 12.062 r_dihedral_angle_1_deg 5.6 r_mcangle_it 2.769 r_mcbond_it 1.783 r_mcbond_other 1.783 r_angle_refined_deg 1.652 r_angle_other_deg 1.26 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.405 r_dihedral_angle_4_deg 17.33 r_dihedral_angle_3_deg 12.062 r_dihedral_angle_1_deg 5.6 r_mcangle_it 2.769 r_mcbond_it 1.783 r_mcbond_other 1.783 r_angle_refined_deg 1.652 r_angle_other_deg 1.26 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1126 Nucleic Acid Atoms 976 Solvent Atoms 64 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing MOLREP phasing