☰ Navigation Tabs
The structure of AfUAP1 in complex with GlcNAc-1P
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 291.15 0.2 M sodium acetate, 25% polyethylene glycol (PEG) 3350
Crystal Properties Matthews coefficient Solvent content 2.54 51.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.834 α = 90 b = 136.865 β = 90 c = 143.081 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 2025-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
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 1.72 71.54 98.2 0.999 15.6 12.7 115021
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 1.72 1.75 0.314
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 1.72 71.54 110112 1925 95.62 0.21112 0.21044 0.2195 0.25186 0.2651 RANDOM 43.559
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] 4.21 -2.22 -1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.23 r_long_range_B_refined 7.655 r_long_range_B_other 7.632 r_dihedral_angle_2_deg 7.219 r_dihedral_angle_1_deg 6.663 r_scangle_other 6.084 r_mcangle_it 4.949 r_mcangle_other 4.948 r_scbond_it 4.099 r_scbond_other 4.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.23 r_long_range_B_refined 7.655 r_long_range_B_other 7.632 r_dihedral_angle_2_deg 7.219 r_dihedral_angle_1_deg 6.663 r_scangle_other 6.084 r_mcangle_it 4.949 r_mcangle_other 4.948 r_scbond_it 4.099 r_scbond_other 4.099 r_mcbond_it 3.6 r_mcbond_other 3.599 r_angle_refined_deg 1.432 r_angle_other_deg 0.475 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 7344 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling PHASER phasing