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MBD2 in complex with methylated DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other currently unpublished model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 20% PEG-3350, 0.2 M ammonium chloride
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.533 α = 83.97 b = 39.875 β = 85.7 c = 105.151 γ = 62.75
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 2013-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 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 2.05 35.34 96.2 0.067 0.09 0.06 0.996 9.6 2.2 31675
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 2.05 2.11 96.8 0.663 0.895 0.597 0.495 2.2
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R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT currently unpublished model 2.05 34.84 30448 1224 96.16 0.2319 0.2305 0.2412 0.2652 0.2741 thin shells (sftools) 36.197
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] -0.01 -0.02 0.2 -0.71 0.11 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.573 r_dihedral_angle_4_deg 19.72 r_dihedral_angle_3_deg 12.377 r_dihedral_angle_1_deg 5.713 r_mcangle_it 1.688 r_angle_refined_deg 1.517 r_angle_other_deg 1.138 r_mcbond_it 1.045 r_mcbond_other 1.039 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.573 r_dihedral_angle_4_deg 19.72 r_dihedral_angle_3_deg 12.377 r_dihedral_angle_1_deg 5.713 r_mcangle_it 1.688 r_angle_refined_deg 1.517 r_angle_other_deg 1.138 r_mcbond_it 1.045 r_mcbond_other 1.039 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2037 Nucleic Acid Atoms 974 Solvent Atoms 115 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing