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VcaM4I restriction endonuclease 5hmC-ssDNA complex
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 8.5 291 Reservoir solution: 1.6 M (NH4)2SO4, 0.1 M MES pH 5.25; protein:DNA solution: 300 mM NaCl, 15 mM Tris-HCl pH 8.5 and 1mM TCEP. For cryo-protection the reservoir solution was diluted with glycerol to achieve 30% concentration. 0.1 M spermine tetrahydrochloride was used as an additive.
Crystal Properties Matthews coefficient Solvent content 3.59 65.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.685 α = 90 b = 128.685 β = 90 c = 110.895 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 EIGER X 16M 2019-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 1.0064 EMBL/DESY, HAMBURG X13
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 1.55 29.77 99.9 0.101 0.103 1 26.96 39.2 78576 30.8
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 1.55 1.64 99.7 2.334 2.364 0.752 1.96 39.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6YEX 1.55 29.77 74619 3912 99.93 0.1436 0.1425 0.1636 0.1596 RANDOM 28.835
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 0.19 0.38 -1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.51 r_dihedral_angle_4_deg 24.457 r_dihedral_angle_3_deg 12.664 r_dihedral_angle_1_deg 6.534 r_angle_other_deg 1.45 r_angle_refined_deg 1.358 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.51 r_dihedral_angle_4_deg 24.457 r_dihedral_angle_3_deg 12.664 r_dihedral_angle_1_deg 6.534 r_angle_other_deg 1.45 r_angle_refined_deg 1.358 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 101 Solvent Atoms 585 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing PDB_EXTRACT data extraction