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Crystal structure of the glycosyltransferase domain of Legionella SetA (unbound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other single-wavelength anomalous diffraction (SAD) of SetA NTD
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 3.13 60.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.413 α = 90 b = 139.413 β = 90 c = 59.944 γ = 120
Symmetry Space Group P 32 2 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 EIGER X 9M 2014-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.9796 PAL/PLS 5C (4A)
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 2.54 42.57 99.9 0.01 48.1 5.5 21215
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.54 2.63 0.01
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 SAD THROUGHOUT 2.54 42.57 21215 1079 99.83 0.19617 0.19349 0.2074 0.24681 0.2524 RANDOM 68.897
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] 0.86 0.43 0.86 -2.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.359 r_long_range_B_refined 9.251 r_long_range_B_other 9.25 r_scangle_other 6.776 r_dihedral_angle_1_deg 6.544 r_mcangle_it 6.187 r_mcangle_other 6.185 r_scbond_it 4.291 r_scbond_other 4.29 r_dihedral_angle_2_deg 4.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.359 r_long_range_B_refined 9.251 r_long_range_B_other 9.25 r_scangle_other 6.776 r_dihedral_angle_1_deg 6.544 r_mcangle_it 6.187 r_mcangle_other 6.185 r_scbond_it 4.291 r_scbond_other 4.29 r_dihedral_angle_2_deg 4.183 r_mcbond_it 4.043 r_mcbond_other 4.043 r_angle_refined_deg 1.033 r_angle_other_deg 0.361 r_chiral_restr 0.049 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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 3608 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHENIX phasing