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YdaS N-terminal domain from prophage CP-933P in E. coli O157:H7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8C7K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 0.024 M 1,6-Hexanediol, 0.024 M 1-Butanol, 0.024 M 1,2-Propanediol, 0.024 M 2-Propanol
0.024 M 1,3-Propanediol, 0.05 M Sodium HEPES, 0.05 M MOPS, 9.375% v/v MPD; 9.375% PEG 1000; 9.375% w/v PEG 3350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.71 α = 90 b = 42.71 β = 90 c = 65.09 γ = 120
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 2022-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 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 1.6388072348 36.9879449956 99.4 0.04 0.999 23.81 10.44 16212 43.4269937054
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 1.6388072348 1.75 99.5 1.135 0.668 1.46 10.1
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.6388072348 36.9879449956 1.95891869141 16212 810 99.3991416309 0.214110437676 0.211857012744 0.2166 0.257643008052 0.2597 59.8461060216
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 16.6246554693 f_angle_d 0.744378057075 f_chiral_restr 0.0439878137398 f_bond_d 0.00514888563458 f_plane_restr 0.00429057527795
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1138 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing