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The structure of Aspergillus fumigatus UDP-GlcNAc pyrophosphorylase in complex with a fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TN3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2 M Sodium acetate
25 % PEG3350
Crystal Properties Matthews coefficient Solvent content 2.54 51.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.37 α = 90 b = 137.5 β = 90 c = 143.66 γ = 90
Symmetry Space Group P 21 21 21
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 XE 16M 2023-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.98 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.87 51.36 99.9 1 16.7 13.2 91430
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.9 0.389
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 1.87 51.36 85508 4580 98.44 0.22807 0.22633 0.2332 0.25903 0.2633 RANDOM 52.998
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] 2.87 -2.77 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.066 r_long_range_B_other 8.695 r_long_range_B_refined 8.694 r_dihedral_angle_2_deg 7.76 r_dihedral_angle_1_deg 6.966 r_scangle_other 6.942 r_mcangle_it 6.064 r_mcangle_other 6.063 r_scbond_it 5.151 r_scbond_other 5.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.066 r_long_range_B_other 8.695 r_long_range_B_refined 8.694 r_dihedral_angle_2_deg 7.76 r_dihedral_angle_1_deg 6.966 r_scangle_other 6.942 r_mcangle_it 6.064 r_mcangle_other 6.063 r_scbond_it 5.151 r_scbond_other 5.151 r_mcbond_it 4.848 r_mcbond_other 4.844 r_angle_refined_deg 1.482 r_angle_other_deg 0.491 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 7268 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing