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MBD2 in complex with a partially methylated DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other currently unpublished model of MBD2-DNA complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 27% PEG-3350, 0.1 M Bis-Tris, 0.15 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.62 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.473 α = 90 b = 36.933 β = 108.25 c = 104.076 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 DECTRIS PILATUS3 6M 2017-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 1.84 49.42 99 0.052 0.063 0.034 0.997 9.8 3.2 22367
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 1.84 1.88 91.3 1.244 1.501 0.828 0.34 3
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(DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT currently unpublished model of MBD2-DNA complex 1.84 49 21271 1095 98.96 0.2153 0.2137 0.2155 0.2468 0.2495 49.509
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] -0.13 -0.06 0.01 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.368 r_dihedral_angle_4_deg 20.662 r_dihedral_angle_3_deg 11.697 r_dihedral_angle_1_deg 6.071 r_mcangle_it 2.027 r_angle_refined_deg 1.758 r_mcbond_other 1.376 r_mcbond_it 1.375 r_angle_other_deg 1.182 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.368 r_dihedral_angle_4_deg 20.662 r_dihedral_angle_3_deg 11.697 r_dihedral_angle_1_deg 6.071 r_mcangle_it 2.027 r_angle_refined_deg 1.758 r_mcbond_other 1.376 r_mcbond_it 1.375 r_angle_other_deg 1.182 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 996 Nucleic Acid Atoms 487 Solvent Atoms 41 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing