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Crystal structure of the methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence in space group P1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VXV PDB ENTRY 3VXV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2mM zinc acetate, 100mM sodium cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.604 α = 75.28 b = 34.093 β = 77.76 c = 61.165 γ = 87.31
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315 2007-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
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 2.5 50 92.8 0.058 16.3 2.9 7786 7225 1 1 35.89
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 2.5 2.59 67.4 0.125 5.4 1.7
Refinement Statistics Diffraction ID Structure Solution 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3VXV 2.525 32.972 0.07 7095 323 90.27 0.1954 0.1934 0.1903 0.2365 0.2276 RANDOM 36.5379
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] -4.2347 -8.443 -4.6272 5.9693 2.7744 -1.7345
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.241 f_angle_d 1.161 f_chiral_restr 0.062 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1030 Nucleic Acid Atoms 429 Solvent Atoms 55 Heterogen Atoms 7
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling