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CpG specific M.MpeI methyltransferase crystallized in the presence of 5,6-dihydro-5-azacytosine (converted to 5m-dhaC) 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 56.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.453 α = 90 b = 84.453 β = 90 c = 172.565 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 2013-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.27820 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 1.95 20 95 0.037 0.043 0.999 18.27 3.66 44130 48.6
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 1.95 2.07 96 0.701 0.822 0.685 1.8 3.58
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 1.95 19.93 41915 2204 95.11 0.16317 0.16167 0.1677 0.19202 0.1988 RANDOM 48.612
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] 0.26 0.26 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.933 r_dihedral_angle_4_deg 15.159 r_dihedral_angle_3_deg 13.564 r_dihedral_angle_1_deg 5.381 r_long_range_B_refined 5.275 r_long_range_B_other 4.598 r_scangle_other 1.588 r_mcangle_it 1.339 r_mcangle_other 1.339 r_angle_refined_deg 1.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.933 r_dihedral_angle_4_deg 15.159 r_dihedral_angle_3_deg 13.564 r_dihedral_angle_1_deg 5.381 r_long_range_B_refined 5.275 r_long_range_B_other 4.598 r_scangle_other 1.588 r_mcangle_it 1.339 r_mcangle_other 1.339 r_angle_refined_deg 1.091 r_scbond_it 0.917 r_scbond_other 0.916 r_angle_other_deg 0.842 r_mcbond_it 0.786 r_mcbond_other 0.786 r_chiral_restr 0.069 r_bond_refined_d 0.005 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 3090 Nucleic Acid Atoms 570 Solvent Atoms 464 Heterogen Atoms 73
Software Software Software Name Purpose XDS data reduction XDS data scaling REFMAC phasing ARP/wARP model building REFMAC refinement PDB_EXTRACT data extraction