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UDP-Glucose-bound UgtP with deletion of Pro48-Met91 and insertion of a Ser-Ser-Ser linker
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 6 293 0.1 M MES, 5% (w/v) PEG6000
Crystal Properties Matthews coefficient Solvent content 2.81 56.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.12 α = 90 b = 64.08 β = 107.234 c = 110.66 γ = 90
Symmetry Space Group C 1 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 4M 2024-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.018 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.7 50 99.4 0.245 0.989 5.49 3.6 9535
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.7 3.9 98.7 1.153 0.612 1.45 3.55
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 3.7 48.045 9535 477 99.52 0.234 0.23 0.2299 0.3105 0.3249 129.425
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] -0.653 -0.21 -0.986 1.483
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.262 r_lrange_it 25.224 r_dihedral_angle_3_deg 23.165 r_dihedral_angle_4_deg 15.22 r_scangle_it 13.823 r_mcangle_it 13.335 r_scbond_it 8.14 r_mcbond_it 7.923 r_dihedral_angle_1_deg 7.738 r_angle_refined_deg 1.671
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.262 r_lrange_it 25.224 r_dihedral_angle_3_deg 23.165 r_dihedral_angle_4_deg 15.22 r_scangle_it 13.823 r_mcangle_it 13.335 r_scbond_it 8.14 r_mcbond_it 7.923 r_dihedral_angle_1_deg 7.738 r_angle_refined_deg 1.671 r_nbtor_refined 0.327 r_symmetry_nbd_refined 0.276 r_nbd_refined 0.271 r_xyhbond_nbd_refined 0.19 r_ncsr_local_group_1 0.189 r_chiral_restr 0.132 r_ext_dist_refined_d 0.112 r_symmetry_xyhbond_nbd_refined 0.072 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5129 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing