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Structure of human O-GlcNAc transferase in complex with UDP and tP11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PE3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1.5 M potassium phosphate dibasic, 5 % xylitol and 10 mM EDTA
Crystal Properties Matthews coefficient Solvent content 4.68 73.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 272.97 α = 90 b = 272.97 β = 90 c = 142.593 γ = 120
Symmetry Space Group P 3 2 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 EIGER2 XE 16M 2021-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 122.1 100 0.286 0.062 0.996 9.3 21.2 149701
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.85 2.647 0.563 0.619 1.4 22
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.8 122.1 142053 7627 99.984 0.198 0.1964 0.1974 0.224 0.2221 58.798
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] 1.269 0.635 1.269 -4.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.488 r_dihedral_angle_4_deg 22.421 r_dihedral_angle_3_deg 16.24 r_lrange_other 11.163 r_lrange_it 11.162 r_scangle_it 8.504 r_scangle_other 8.501 r_mcangle_it 7.421 r_mcangle_other 7.421 r_dihedral_angle_1_deg 6.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.488 r_dihedral_angle_4_deg 22.421 r_dihedral_angle_3_deg 16.24 r_lrange_other 11.163 r_lrange_it 11.162 r_scangle_it 8.504 r_scangle_other 8.501 r_mcangle_it 7.421 r_mcangle_other 7.421 r_dihedral_angle_1_deg 6.624 r_scbond_it 5.859 r_scbond_other 5.852 r_mcbond_it 5.187 r_mcbond_other 5.186 r_angle_refined_deg 1.544 r_angle_other_deg 1.422 r_nbd_refined 0.219 r_symmetry_nbd_refined 0.218 r_symmetry_nbd_other 0.187 r_nbd_other 0.176 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.142 r_xyhbond_nbd_refined 0.141 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.068 r_ncsr_local_group_5 0.059 r_ncsr_local_group_1 0.057 r_ncsr_local_group_4 0.057 r_ncsr_local_group_2 0.056 r_ncsr_local_group_3 0.056 r_ncsr_local_group_6 0.055 r_symmetry_xyhbond_nbd_other 0.045 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22072 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing