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Crystal structure of diphtheria toxin mutant CRM197 with a disulphide bond replaced by a Cys-Acetone-Cys bridge
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AE0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291.15 0.1 M sodium cacodylate, 0.2 M magnesium acetate, 20% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.33 47.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.996 α = 90 b = 97.996 β = 90 c = 98.267 γ = 120
Symmetry Space Group P 31 1 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 2018-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9762 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.03 49 100 0.051 0.999 26.22 11.2 35072 49.9066061092
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.103 1.225 0.711 2.11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT FREE R-VALUE 4AE0 2.03002061079 48.99795 1.35509021097 35037 1716 99.9771722072 0.205820694042 0.204160409163 0.2118 0.237125486782 0.2401 54.5854607343
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 19.5835844189 f_angle_d 1.21115009624 f_chiral_restr 0.0754226678536 f_bond_d 0.0197239359424 f_plane_restr 0.00765616160093
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3940 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing