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Crystal structure of Tlde1a from Salmonella Typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other NaI derivative solved using SAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 12mg/ml Tlde1a,
15% PEG 3350,
0.2M Ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.32 46.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.381 α = 90 b = 59.381 β = 90 c = 105.125 γ = 90
Symmetry Space Group P 41 21 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 IMAGE PLATE RIGAKU RAXIS IV++ 2021-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 41.99 99.6 0.06 0.017 0.999 25.9 13.2 25343 17.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 92.2 0.525
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 FOURIER SYNTHESIS FREE R-VALUE NaI derivative solved using SAD 1.6 29.69 1.38 25275 1227 99.74 0.1661 0.165 0.165 0.1873 0.1878 26.31
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 13.5863 f_angle_d 0.9338 f_chiral_restr 0.0646 f_bond_d 0.009 f_plane_restr 0.0088
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1391 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling AutoSol phasing PHENIX phasing Coot model building