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Structure of SenB in complex with UDP-GlcNAc at 1.88 Angstroms resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.153 15% PEG 20000, 0.1M Hepes/NaOH pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.12 60.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.223 α = 90 b = 56.375 β = 91.106 c = 108.445 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 PILATUS3 6M 2023-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.88 48.85 99.8 0.998 15.2 6.6 106627
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 1.88 1.91 0.771
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.88 48.848 106588 4962 94.183 0.188 0.1865 0.1912 0.2149 0.2208 27.259
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] 3.959 6.614 -11.483 7.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.253 r_dihedral_angle_4_deg 19.133 r_dihedral_angle_3_deg 15.01 r_dihedral_angle_1_deg 7.183 r_lrange_it 6.479 r_lrange_other 6.345 r_scangle_it 4.698 r_scangle_other 4.697 r_mcangle_it 3.484 r_mcangle_other 3.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.253 r_dihedral_angle_4_deg 19.133 r_dihedral_angle_3_deg 15.01 r_dihedral_angle_1_deg 7.183 r_lrange_it 6.479 r_lrange_other 6.345 r_scangle_it 4.698 r_scangle_other 4.697 r_mcangle_it 3.484 r_mcangle_other 3.484 r_scbond_it 3.316 r_scbond_other 3.315 r_mcbond_it 2.666 r_mcbond_other 2.666 r_angle_refined_deg 1.818 r_angle_other_deg 1.418 r_nbd_refined 0.207 r_symmetry_nbd_refined 0.192 r_symmetry_nbd_other 0.186 r_symmetry_xyhbond_nbd_refined 0.183 r_xyhbond_nbd_refined 0.177 r_symmetry_xyhbond_nbd_other 0.175 r_nbtor_refined 0.155 r_nbd_other 0.138 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7223 Nucleic Acid Atoms Solvent Atoms 810 Heterogen Atoms 117
Software Software Software Name Purpose Blu-Ice data collection XDS data reduction Aimless data scaling PHENIX phasing