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Crystal structure of the C-terminal domain of human N-acetylglucosaminyltransferase IVa
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 293 0.2 M lithium nitrate, 20%(w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 1.82 32.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.699 α = 90 b = 32.49 β = 94.71 c = 85.629 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 6M 2022-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.97 85.34 100 0.207 0.216 0.06 0.99 8.4 12.8 20101
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 1.97 2.08 100 0.822 0.855 0.234 0.951 2.4 13
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 1.972 50.579 20082 959 99.945 0.223 0.2204 0.2276 0.2663 0.2673 61.557
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] 2.945 -0.197 2.991 -5.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.939 r_dihedral_angle_3_deg 15.361 r_dihedral_angle_4_deg 13.427 r_dihedral_angle_1_deg 8.117 r_lrange_it 6.605 r_lrange_other 6.601 r_scangle_it 4.735 r_scangle_other 4.733 r_mcangle_other 4.182 r_mcangle_it 4.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.939 r_dihedral_angle_3_deg 15.361 r_dihedral_angle_4_deg 13.427 r_dihedral_angle_1_deg 8.117 r_lrange_it 6.605 r_lrange_other 6.601 r_scangle_it 4.735 r_scangle_other 4.733 r_mcangle_other 4.182 r_mcangle_it 4.181 r_scbond_it 3.21 r_scbond_other 3.209 r_mcbond_it 2.969 r_mcbond_other 2.961 r_angle_refined_deg 1.704 r_angle_other_deg 1.265 r_nbd_refined 0.2 r_nbd_other 0.189 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.102 r_symmetry_nbd_refined 0.092 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.074 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2331 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing Coot model building