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The active site of O-GlcNAc transferase imposes constraints on substrate sequence
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PE4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 294 1.3 M DL-Malic acid pH 6.4, 0.1 M Bis-Tris propane pH 6.4 supplemented with crystal seeds grown out of the same condition.
Crystal Properties Matthews coefficient Solvent content 2.21 44.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.183 α = 90 b = 150.176 β = 90 c = 199.241 γ = 90
Symmetry Space Group F 2 2 2
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 PSI PILATUS 6M Pilatus 2M Detector 2015-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 30 99.9 0.104 11.8 6.5 263631 40463
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 100 0.719 2.4 6.7
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 (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 3PE4 2.4 30 38435 2022 99.84 0.18981 0.18736 0.1935 0.23517 0.2387 RANDOM 45.84
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] -1.49 2.89 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.512 r_dihedral_angle_4_deg 18.421 r_dihedral_angle_3_deg 15.779 r_long_range_B_other 7.577 r_long_range_B_refined 7.573 r_dihedral_angle_1_deg 6.366 r_scangle_other 5.515 r_mcangle_it 4.584 r_mcangle_other 4.584 r_scbond_it 3.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.512 r_dihedral_angle_4_deg 18.421 r_dihedral_angle_3_deg 15.779 r_long_range_B_other 7.577 r_long_range_B_refined 7.573 r_dihedral_angle_1_deg 6.366 r_scangle_other 5.515 r_mcangle_it 4.584 r_mcangle_other 4.584 r_scbond_it 3.424 r_scbond_other 3.423 r_mcbond_it 3.027 r_mcbond_other 3.027 r_angle_refined_deg 1.492 r_angle_other_deg 0.82 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 5533 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling Coot model building MOLREP phasing