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Crystal structure of the L. monocytogenes RmlT in complex with TDP-rhamnose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BZ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Bis-Tris propane pH 7.0
0.2 M Potassium sodium tartrate tetrahydrate
20% (w/v) PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.69 54.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.988 α = 90 b = 291.265 β = 100.379 c = 92.394 γ = 90
Symmetry Space Group P 1 21 1
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 2020-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979257 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.2 50 99.8 0.059 0.059 0.069 0.035 0.999 14 3.8 227206 46.28
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) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 1.087 1.087 1.275 0.658 0.555 1.2
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 8BZ4 2.2 50 1.35 227111 11129 99.73 0.1887 0.1873 0.1874 0.215 0.2152 57.86
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 24.2621 f_angle_d 0.6703 f_chiral_restr 0.2806 f_bond_d 0.0046 f_plane_restr 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29172 Nucleic Acid Atoms Solvent Atoms 1193 Heterogen Atoms 317
Software Software Software Name Purpose PHENIX refinement XDS data scaling PHASER phasing XDS data reduction