☰ Navigation Tabs
CpG specific M.MpeI methyltransferase crystallized in the presence of 5-bromocytosine (converted to 5mC) and 5-methylcytosine containing dsDNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 294 10% PEG 3350, 150 mM NaCl, 50 mM sodium citrate (final pH, 5.6). For cryoprotection glycerol was added to 25% v/v
Crystal Properties Matthews coefficient Solvent content 2.8 56.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.511 α = 90 b = 84.511 β = 90 c = 173.115 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS 6M-F 2016-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.91160 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 1.7 20 99.8 0.039 0.041 1 27.87 8.78 69838 38.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.8 99.8 0.919 0.98 0.822 2.15 8.52
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 4dkj 1.7 19.95 66340 3498 99.83 0.16782 0.16652 0.1749 0.19278 0.2019 RANDOM 38.536
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] 0.38 0.38 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.653 r_dihedral_angle_4_deg 14.068 r_dihedral_angle_3_deg 13.037 r_long_range_B_refined 5.938 r_dihedral_angle_1_deg 5.595 r_long_range_B_other 5.083 r_scangle_other 1.342 r_mcangle_it 1.19 r_mcangle_other 1.19 r_angle_refined_deg 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.653 r_dihedral_angle_4_deg 14.068 r_dihedral_angle_3_deg 13.037 r_long_range_B_refined 5.938 r_dihedral_angle_1_deg 5.595 r_long_range_B_other 5.083 r_scangle_other 1.342 r_mcangle_it 1.19 r_mcangle_other 1.19 r_angle_refined_deg 1.14 r_angle_other_deg 0.818 r_scbond_it 0.778 r_scbond_other 0.778 r_mcbond_it 0.679 r_mcbond_other 0.679 r_chiral_restr 0.071 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 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 3107 Nucleic Acid Atoms 570 Solvent Atoms 591 Heterogen Atoms 99
Software Software Software Name Purpose XDS data reduction XDS data scaling REFMAC phasing ARP/wARP model building REFMAC refinement PDB_EXTRACT data extraction