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mbd of human mecp2 in complex with methylated DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C2I Protein coordinates from PDB entry 3c2i. DNA coordinates from a currently unpublished model.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 291 25% PEG3350, 0.1 M ammonium sulfate, 0.1 M tris
Crystal Properties Matthews coefficient Solvent content 2.57 52.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.753 α = 68.15 b = 47.359 β = 89.83 c = 54.623 γ = 65.98
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 2013-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97945 APS 23-ID-B
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 2.3 39.85 96.3 0.068 0.091 0.06 0.992 10.1 2.2 14585
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 2.3 2.38 84.2 0.449 0.601 0.397 0.718 2.1
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Protein coordinates from PDB entry 3c2i. DNA coordinates from a currently unpublished model. 2.3 39.85 13799 785 96.3 0.2334 0.2306 0.2372 0.2857 0.2927 65.544
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] -4.22 -1.93 1.86 1.74 -2.26 -2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.819 r_dihedral_angle_4_deg 28.612 r_dihedral_angle_3_deg 15.157 r_dihedral_angle_1_deg 5.819 r_mcangle_it 3.472 r_mcbond_other 2.296 r_mcbond_it 2.294 r_angle_refined_deg 1.669 r_angle_other_deg 1.316 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.819 r_dihedral_angle_4_deg 28.612 r_dihedral_angle_3_deg 15.157 r_dihedral_angle_1_deg 5.819 r_mcangle_it 3.472 r_mcbond_other 2.296 r_mcbond_it 2.294 r_angle_refined_deg 1.669 r_angle_other_deg 1.316 r_chiral_restr 0.089 r_bond_refined_d 0.016 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 1090 Nucleic Acid Atoms 976 Solvent Atoms Heterogen Atoms 3
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing