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Salmonella Typhimurium ArnD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 Crystals of ArnD were obtained by mixing 2 uL of a stock solution of ArnD (6 mg/mL) in 25mM Tris-HCl, pH8.0, 150mM NaCl, 10% glycerol, 5mM BME, 0.0174% DDM, with 2 uL of a precipitant solution containing 0.1M Na citrate pH 6.2, 10% isopropanol and 17% PEG4000 and allowing vapor diffusion between the protein droplet and a 1mL reservoir of precipitant in a hanging drop set up incubated at 16 degrees Celsius.
Crystal Properties Matthews coefficient Solvent content 3 59.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.551 α = 90 b = 85.646 β = 90 c = 111.91 γ = 90
Symmetry Space Group I 2 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 CCD ADSC QUANTUM 315 2008-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9791 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.59 40.74 91.44 0.0816 0.1012 0.05888 0.995 12.82 2.7 11633 36.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.683 70.43 0.2342 0.2924 0.1725 0.939 3.99 2.5
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.59 40.74 1.36 11587 578 91.32 0.2284 0.2254 0.2265 0.2873 0.2855 42.01
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 17.4098 f_angle_d 0.9703 f_chiral_restr 0.0502 f_plane_restr 0.0088 f_bond_d 0.0074
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2084 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose PHENIX phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling