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Crystal structure MBD3 MBD domain in complex with methylated CpG DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 15% PEG 8000,0.2M magnesium chloride, 0.1M Tris
Crystal Properties Matthews coefficient Solvent content 2.8 55.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.27 α = 90 b = 36.46 β = 92.42 c = 130.84 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 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 1.9 35.18 99.9 0.068 0.074 0.029 0.999 16.7 5.7 27299
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 1.9 1.94 99.8 1.098 1.285 0.662 0.615 3.7 1749
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 35.1 25763 1536 99.84 0.2247 0.2232 0.2315 0.2501 0.2547 thin shells (sftools) 43.018
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] -1.14 0.33 1.39 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.59 r_dihedral_angle_4_deg 16.751 r_dihedral_angle_3_deg 10.306 r_dihedral_angle_1_deg 5.368 r_mcangle_it 2.202 r_angle_refined_deg 1.543 r_mcbond_other 1.362 r_mcbond_it 1.361 r_angle_other_deg 1.19 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.59 r_dihedral_angle_4_deg 16.751 r_dihedral_angle_3_deg 10.306 r_dihedral_angle_1_deg 5.368 r_mcangle_it 2.202 r_angle_refined_deg 1.543 r_mcbond_other 1.362 r_mcbond_it 1.361 r_angle_other_deg 1.19 r_chiral_restr 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1144 Nucleic Acid Atoms 976 Solvent Atoms 88 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing