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MeCP2 MBD domain (A140V) in complex with methylated DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 30% PEG 2000, 200 mM ammonium acetate, 10 mM magnesium acetate, 50 mM sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.18 43.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.66 α = 90 b = 53.49 β = 132.47 c = 65.78 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 PIXEL PSI PILATUS 6M 2012-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 48.5 98.9 9.2 3.8 10482
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 3C2I 2.2 48.5 9955 525 98.7 0.1773 0.1746 0.1817 0.2266 0.2234 RANDOM 73.464
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] 3.12 1.92 -3.4 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.287 r_dihedral_angle_4_deg 26.745 r_dihedral_angle_3_deg 19.85 r_dihedral_angle_1_deg 8.441 r_mcangle_it 4.709 r_mcbond_it 3.399 r_mcbond_other 3.399 r_angle_refined_deg 1.83 r_angle_other_deg 1.372 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.287 r_dihedral_angle_4_deg 26.745 r_dihedral_angle_3_deg 19.85 r_dihedral_angle_1_deg 8.441 r_mcangle_it 4.709 r_mcbond_it 3.399 r_mcbond_other 3.399 r_angle_refined_deg 1.83 r_angle_other_deg 1.372 r_chiral_restr 0.092 r_gen_planes_refined 0.013 r_bond_refined_d 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 572 Nucleic Acid Atoms 816 Solvent Atoms 141 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data collection SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction SCALA data reduction MOLREP phasing