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CpG specific M.MpeI methyltransferase crystallized in the presence of 2'-deoxy-5-methylzebularine (5mZ) 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 2.81 56.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.259 α = 90 b = 84.259 β = 90 c = 173.883 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 2013-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
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 2.4 20 99.6 0.114 0.121 0.999 16.89 8.6 25251 53.298
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 2.4 2.54 99 1.203 1.277 0.703 2.05 8.8
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 4DKJ 2.4 19.89 23997 1253 99.56 0.17535 0.17326 0.1763 0.21625 0.2171 RANDOM 51.84
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] 0.58 0.58 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.755 r_dihedral_angle_4_deg 14.394 r_dihedral_angle_3_deg 14.346 r_dihedral_angle_1_deg 5.523 r_long_range_B_refined 3.77 r_long_range_B_other 3.279 r_mcangle_it 1.187 r_mcangle_other 1.187 r_angle_refined_deg 1.006 r_scangle_other 0.951
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.755 r_dihedral_angle_4_deg 14.394 r_dihedral_angle_3_deg 14.346 r_dihedral_angle_1_deg 5.523 r_long_range_B_refined 3.77 r_long_range_B_other 3.279 r_mcangle_it 1.187 r_mcangle_other 1.187 r_angle_refined_deg 1.006 r_scangle_other 0.951 r_angle_other_deg 0.795 r_mcbond_it 0.646 r_mcbond_other 0.643 r_scbond_it 0.52 r_scbond_other 0.52 r_chiral_restr 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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 3199 Nucleic Acid Atoms 569 Solvent Atoms 412 Heterogen Atoms 33
Software Software Software Name Purpose XDS data reduction XDS data scaling REFMAC phasing ARP/wARP model building REFMAC refinement PDB_EXTRACT data extraction