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Crystal structure of HEPN(H107A-Y109F) toxin in complex with MNT antitoxin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 Crystallization buffer was 0,1 M MES-imidazole pH 6.5, 10% PEG 20K, 20% PEG550MME, 30 mM NaNO3, 30 mM Na2HPO4, 30 mM(NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.2 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.709 α = 90 b = 85.989 β = 90 c = 100.105 γ = 90
Symmetry Space Group C 2 2 21
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 PSI PILATUS 6M 2018-05-17 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL PSI PILATUS 6M 2018-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.3862 PETRA III, EMBL c/o DESY P13 (MX1) 2 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.979600 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) Rpim I (All) 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 55.521 99.9 0.041 0.049 0.019 22.3 6.4 21539 21539 41.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 99.9 0.458 0.458 0.529 0.206 1.5 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2 50.053 0.26 21501 4098 99.56 0.2019 0.1992 0.2089 0.2266 0.2338 58.0177
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.94 f_angle_d 0.437 f_chiral_restr 0.038 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2184 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling SHELXDE phasing PDB_EXTRACT data extraction