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Crystal structure of the C-terminal domain of Bombyx mori N-acetylglucosaminyltransferase IV in complex with N-acetylglucosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold2 model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1 M MES-NaOH, pH 7.0, 12%(w/v) PEG20000, 10 mM N-acetylglucosamine
Crystal Properties Matthews coefficient Solvent content 2.17 43.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.697 α = 90 b = 64.098 β = 95.891 c = 79.148 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 2M 2021-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.15 39.37 98.6 0.046 0.05 0.019 0.999 18.1 6.7 113597
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 1.15 1.21 94.9 0.81 0.879 0.336 0.782 2.3 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 AlphaFold2 model 1.15 32.545 113579 5719 98.625 0.194 0.1933 0.2023 0.2087 0.2191 18.769
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] 0.534 -0.401 0.215 -0.653
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.022 r_dihedral_angle_4_deg 18.822 r_dihedral_angle_3_deg 12.612 r_dihedral_angle_1_deg 7.733 r_lrange_it 4.199 r_lrange_other 4.096 r_scangle_it 1.998 r_scangle_other 1.998 r_angle_refined_deg 1.677 r_angle_other_deg 1.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.022 r_dihedral_angle_4_deg 18.822 r_dihedral_angle_3_deg 12.612 r_dihedral_angle_1_deg 7.733 r_lrange_it 4.199 r_lrange_other 4.096 r_scangle_it 1.998 r_scangle_other 1.998 r_angle_refined_deg 1.677 r_angle_other_deg 1.423 r_mcangle_it 1.317 r_mcangle_other 1.317 r_scbond_it 1.264 r_scbond_other 1.263 r_mcbond_it 0.811 r_mcbond_other 0.81 r_symmetry_nbd_refined 0.239 r_nbd_other 0.209 r_nbd_refined 0.2 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.143 r_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2494 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing Coot model building