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Crystal structure of the glycosyltransferase domain of Legionella SetA in complex with UPD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8X4J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 287 6% (v/v) MPD, 14% (w/v) PEG 4,000, and 0.1 M sodium/potassium phosphate at pH 6.2
Crystal Properties Matthews coefficient Solvent content 2.21 44.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.823 α = 90 b = 62.795 β = 90 c = 176.663 γ = 90
Symmetry Space Group P 21 21 21
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 9M 2019-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.9794 PAL/PLS 11C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.79 29.6 98.6 0.132 15.5 4.86 44091
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.9 0.463
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.79 29.6 41930 2094 98.54 0.20185 0.20054 0.2064 0.22814 0.2393 RANDOM 26.524
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] 1.68 -0.92 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.902 r_dihedral_angle_1_deg 5.926 r_dihedral_angle_2_deg 4.79 r_long_range_B_refined 4.138 r_long_range_B_other 4.053 r_mcangle_it 2.011 r_mcangle_other 2.011 r_scangle_other 1.907 r_mcbond_it 1.146 r_mcbond_other 1.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.902 r_dihedral_angle_1_deg 5.926 r_dihedral_angle_2_deg 4.79 r_long_range_B_refined 4.138 r_long_range_B_other 4.053 r_mcangle_it 2.011 r_mcangle_other 2.011 r_scangle_other 1.907 r_mcbond_it 1.146 r_mcbond_other 1.145 r_scbond_it 1.126 r_scbond_other 1.126 r_angle_refined_deg 0.83 r_angle_other_deg 0.301 r_chiral_restr 0.044 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3633 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHENIX phasing