☰ Navigation Tabs
Crystal structure of WT hMBD4 complexed with T:G mismatch DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 15% PEG1500
0.1 M MES pH 6.5
0.2 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.46 49.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.35 α = 90 b = 58.433 β = 90 c = 101.142 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 120 PIXEL DECTRIS PILATUS3 6M 2019-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.98 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.01 50 97.7 0.031 27.9 9.8 15766
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.04 0.524 0.728
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4E9G 2.02 38.24 15588 815 96.04 0.2189 0.2231 0.2634 0.2672 52.45
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 25.661 f_angle_d 1.0848 f_chiral_restr 0.0515 f_bond_d 0.0089 f_plane_restr 0.0056
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1179 Nucleic Acid Atoms 479 Solvent Atoms 46 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing