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Crystal structure of the C-terminal domain of Bombyx mori N-acetylglucosaminyltransferase IV
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
Crystal Properties Matthews coefficient Solvent content 2.17 43.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.733 α = 90 b = 64.466 β = 95.092 c = 78.81 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 S 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 1.47 39.25 96.6 0.052 0.057 0.022 0.999 18.2 6.4 53654
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 1.47 1.55 83 0.526 0.588 0.255 0.841 2.7 5
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 1.47 33.547 53581 2686 96.454 0.226 0.2244 0.2314 0.2484 0.2534 21.258
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] -0.6 0.134 -1.848 2.386
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.856 r_dihedral_angle_3_deg 12.794 r_dihedral_angle_4_deg 12.439 r_dihedral_angle_1_deg 8.001 r_lrange_it 4.226 r_lrange_other 4.203 r_scangle_it 1.803 r_scangle_other 1.802 r_angle_refined_deg 1.729 r_angle_other_deg 1.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.856 r_dihedral_angle_3_deg 12.794 r_dihedral_angle_4_deg 12.439 r_dihedral_angle_1_deg 8.001 r_lrange_it 4.226 r_lrange_other 4.203 r_scangle_it 1.803 r_scangle_other 1.802 r_angle_refined_deg 1.729 r_angle_other_deg 1.457 r_mcangle_it 1.337 r_mcangle_other 1.337 r_scbond_it 1.151 r_scbond_other 1.151 r_mcbond_it 0.82 r_mcbond_other 0.814 r_nbd_refined 0.203 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.141 r_nbd_other 0.141 r_symmetry_xyhbond_nbd_refined 0.117 r_symmetry_nbd_refined 0.116 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2317 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing Coot model building