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Crystal structure of MBD2 complex with methylated CpG island
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2KY8 pdb entries 2KY8, 3QMG experimental model PDB 3QMG pdb entries 2KY8, 3QMG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 8% PEG550MME, 8% PEG20000, 0.2M calcium acetate
Crystal Properties Matthews coefficient Solvent content 3.2 60.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.96 α = 101.57 b = 41.32 β = 99.46 c = 58.67 γ = 100.54
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 MARMOSAIC 300 mm CCD 2011-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97947 APS 23-ID-D
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 2.1 39.46 97.8 0.044 0.051 0.026 0.998 15.3 3.9 20704 50.39
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 2.1 2.16 97.2 0.97 1.122 0.563 0.685 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE pdb entries 2KY8, 3QMG 2.1 39.457 1.92 40927 2109 96.72 0.1906 0.189 0.1964 0.2177 0.2266 61.2521
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 946 Nucleic Acid Atoms 976 Solvent Atoms 34 Heterogen Atoms 12
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing