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Structure of wild-type human MBD4 bound to a G:T mismatch
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OFA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 21% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.01 36.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.886 α = 90 b = 54.875 β = 90 c = 104.522 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315r 2014-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97648 ALS 5.0.3
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 1.83 38.91 97.7 0.071 30.7 6.9 20686
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 1.83 1.895 96.8 0.544 3.15 6.8
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 4OFA 1.83 38.91 19653 1067 94.28 0.17546 0.17369 0.1836 0.20899 0.2154 RANDOM 26.669
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] 0.35 0.09 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.242 r_dihedral_angle_4_deg 24.644 r_dihedral_angle_3_deg 15.573 r_long_range_B_refined 6.982 r_long_range_B_other 6.981 r_dihedral_angle_1_deg 5.629 r_scangle_other 5.288 r_scbond_other 3.725 r_scbond_it 3.724 r_mcangle_it 2.804
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.242 r_dihedral_angle_4_deg 24.644 r_dihedral_angle_3_deg 15.573 r_long_range_B_refined 6.982 r_long_range_B_other 6.981 r_dihedral_angle_1_deg 5.629 r_scangle_other 5.288 r_scbond_other 3.725 r_scbond_it 3.724 r_mcangle_it 2.804 r_mcangle_other 2.802 r_mcbond_it 2.05 r_mcbond_other 2.022 r_angle_refined_deg 1.766 r_angle_other_deg 1.055 r_chiral_restr 0.107 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1196 Nucleic Acid Atoms 488 Solvent Atoms 156 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOLREP phasing HKL-2000 data scaling HKL-2000 data reduction