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The Crystal Structure of Methyl-CpG Binding Domain of Human MeCP2 in Complex with a Methylated DNA Sequence from BDNF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 26% PEG2000, 0.2M Ammonium acetate, 0.01M Mg acetate, 0.05M Na cacodylate pH6.5, 0.002M DTT, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.21 44.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.71 α = 90 b = 53.6 β = 132.1 c = 65.73 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 MARMOSAIC 225 mm CCD mirrors 2006-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97800 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 48.795 98.5 0.075 0.075 3.1 7.1 7122 7122 84.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 90.7 0.377 0.377 2 5.3 950
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 2.5 23.48 7115 7115 331 98.53 0.215 0.212 0.2069 0.276 0.2679 RANDOM 59.076
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] 0.29 0.07 0.3 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.425 r_dihedral_angle_4_deg 21.077 r_dihedral_angle_3_deg 20.454 r_dihedral_angle_1_deg 5.524 r_angle_refined_deg 1.848 r_scangle_it 1.579 r_scbond_it 1.001 r_mcangle_it 0.898 r_mcbond_it 0.693 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.425 r_dihedral_angle_4_deg 21.077 r_dihedral_angle_3_deg 20.454 r_dihedral_angle_1_deg 5.524 r_angle_refined_deg 1.848 r_scangle_it 1.579 r_scbond_it 1.001 r_mcangle_it 0.898 r_mcbond_it 0.693 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.189 r_symmetry_hbond_refined 0.129 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 584 Nucleic Acid Atoms 816 Solvent Atoms 47 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction