☰ Navigation Tabs
Crystal structure of DNMT3B(Q772R)-DNMT3L in complex with CpGpT DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YX2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277.15 0.1 M Tris-HCl (pH 8.0), 200 mM MgCl2, 8% PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.99 69.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 190.344 α = 90 b = 190.344 β = 90 c = 49.644 γ = 120
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 2018-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.99998872297 47.59 99.7 0.99 6.76 8.2 40256 64.1976072599
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 98.1 1.36 0.704 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 5YX2 2.99998872297 47.586 1.95924514285 40179 2018 99.6948042281 0.216782524271 0.214549750174 0.2134 0.25910047627 0.2569 75.9153995093
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 21.3929201931 f_angle_d 0.652710535631 f_chiral_restr 0.0417668523331 f_bond_d 0.00429220153937 f_plane_restr 0.00393491502471
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7493 Nucleic Acid Atoms 1020 Solvent Atoms 32 Heterogen Atoms 55
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing