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VcaM4I restriction endonuclease in the presence of 5mC-modified ssDNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YJB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.25 291 RESERVOIR SOLUTION: 1.6 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 3.61 65.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129 α = 90 b = 129 β = 90 c = 110.911 γ = 120
Symmetry Space Group P 62 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-F 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97626 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 1.48 42.23 98.9 0.091 0.096 0.999 14.95 10.6 90208 26.7
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 1.48 1.56 98.5 0.967 1.019 0.742 1.91 10.1
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 6YJB 1.48 42.23 85724 4481 98.87 0.1702 0.1693 0.1688 0.1881 0.1877 RANDOM 23.433
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] 0.72 0.36 0.72 -2.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.11 r_dihedral_angle_4_deg 20.085 r_dihedral_angle_3_deg 13.63 r_dihedral_angle_1_deg 6.436 r_angle_other_deg 1.384 r_angle_refined_deg 1.288 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.11 r_dihedral_angle_4_deg 20.085 r_dihedral_angle_3_deg 13.63 r_dihedral_angle_1_deg 6.436 r_angle_other_deg 1.384 r_angle_refined_deg 1.288 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2499 Nucleic Acid Atoms 100 Solvent Atoms 589 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PDB_EXTRACT data extraction REFMAC phasing