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Crystal structure of the glycosyltransferase domain of Legionella SetA in complex with UPDGlc
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 2.34 47.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.14 α = 90 b = 63.257 β = 90 c = 184.962 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 2019-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9999 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.9 44.2 99.9 0.063 0.073 0.9990000000000001 12.19 3.97 38012
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2.01 1.008 1.163 0.51
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 1.9 44.19 38012 2005 99.74 0.17667 0.1748 0.1865 0.21058 0.2175 RANDOM 41.751
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] 0.54 0.76 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.411 r_long_range_B_other 8.556 r_long_range_B_refined 8.555 r_dihedral_angle_2_deg 7.813 r_scangle_other 6.837 r_dihedral_angle_1_deg 6.387 r_mcangle_it 4.945 r_mcangle_other 4.945 r_scbond_it 4.625 r_scbond_other 4.604
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.411 r_long_range_B_other 8.556 r_long_range_B_refined 8.555 r_dihedral_angle_2_deg 7.813 r_scangle_other 6.837 r_dihedral_angle_1_deg 6.387 r_mcangle_it 4.945 r_mcangle_other 4.945 r_scbond_it 4.625 r_scbond_other 4.604 r_mcbond_it 3.51 r_mcbond_other 3.505 r_angle_refined_deg 1.392 r_angle_other_deg 0.455 r_chiral_restr 0.064 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 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 3643 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data scaling HKL-2000 data reduction PHENIX phasing