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Crystal structure of SrUGT76G4 in complex with UDP-glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Robetta
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 5.5 293 0.2 M NaSCN, 0.1 M NaCitrate pH5.5, 10-35% PEG3350, 8% D-Sorbitol
Crystal Properties Matthews coefficient Solvent content 2.12 41.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.78 α = 90 b = 111.78 β = 90 c = 91.77 γ = 120
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 EIGER2 S 9M 2023-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.8 33.99 96.1 0.248 0.267 0.094 0.971 5.4 6.9 30343
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 86.3 0.912 1.003 0.397 0.554 5.1
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 2.8 33.99 28750 1560 95.98 0.27244 0.26806 0.2702 0.35122 0.3499 RANDOM 55.168
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] 0.27 0.13 0.27 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.263 r_long_range_B_refined 9.165 r_long_range_B_other 9.164 r_dihedral_angle_1_deg 8.477 r_dihedral_angle_2_deg 6.362 r_mcangle_it 6.04 r_mcangle_other 6.039 r_scangle_other 5.234 r_mcbond_it 3.675 r_mcbond_other 3.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.263 r_long_range_B_refined 9.165 r_long_range_B_other 9.164 r_dihedral_angle_1_deg 8.477 r_dihedral_angle_2_deg 6.362 r_mcangle_it 6.04 r_mcangle_other 6.039 r_scangle_other 5.234 r_mcbond_it 3.675 r_mcbond_other 3.675 r_scbond_it 3.101 r_scbond_other 3.1 r_angle_refined_deg 1.325 r_angle_other_deg 0.459 r_chiral_restr 0.06 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 9354 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOSFLM data reduction MOLREP phasing