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VcaM4I restriction endonuclease in complex with 5mC-modified dsDNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YEX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.25 291 Reservoir solution: 1.2 M (NH4)2SO4 , 0.1 M MES pH 5.25; protein:DNA solution: 0.3 M NaCl, 15 mM Tris-HCl pH 8.5 and 1 mM TCEP. For cryo-protection the reservoir solution was diluted with glycerol to achieve 30% concentration.
Crystal Properties Matthews coefficient Solvent content 3.48 64.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.111 α = 90 b = 81.111 β = 90 c = 617.307 γ = 120
Symmetry Space Group P 61 2 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 2020-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 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 3.14 49.1 92.8 0.215 0.227 0.991 8.6 9.6 20874 54.3
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 3.14 3.33 74.4 1.521 1.641 0.306 0.89 5.2
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 6YEX 3.14 49.1 19843 1031 92.79 0.2428 0.2415 0.2442 0.2662 0.2659 RANDOM 71.579
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] -0.76 -0.38 -0.76 2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.543 r_dihedral_angle_3_deg 13.924 r_dihedral_angle_4_deg 11.394 r_dihedral_angle_1_deg 7.137 r_angle_refined_deg 1.193 r_angle_other_deg 1.173 r_chiral_restr 0.046 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.543 r_dihedral_angle_3_deg 13.924 r_dihedral_angle_4_deg 11.394 r_dihedral_angle_1_deg 7.137 r_angle_refined_deg 1.193 r_angle_other_deg 1.173 r_chiral_restr 0.046 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4998 Nucleic Acid Atoms 892 Solvent Atoms 86 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing