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The human O-GlcNAc transferase in complex with a thiol-linked bisubstrate inhibitor
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 6.4 295 Reservoir solution: 1.45 M K2HPO4, 8 mM EDTA, 1% xylitol
Drop solution: 1.45 M K2HPO4, 8 mM EDTA, 1% xylitol, 0.5 M (NH4)2SO4, crystal seeds
Seeds were generated from crystals grown in 1.3 M DL-Malic acid, 0.1 M Bis-Tris propane pH 6.4
Crystal Properties Matthews coefficient Solvent content 3.33 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.038 α = 90 b = 150.951 β = 90 c = 200.54 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 DECTRIS PILATUS 6M 2014-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.85 46.01 99.5 0.06 0.078 0.048 0.99 9.7 4 88158
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 99.8 0.871 1.202 0.711 0.65 1.3 4.1
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 1.85 46.01 83781 4369 99.42 0.2065 0.20497 0.2196 0.23641 0.2554 RANDOM 46.58
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] -2.79 4.54 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.605 r_dihedral_angle_4_deg 18.311 r_dihedral_angle_3_deg 13.492 r_long_range_B_refined 6.534 r_long_range_B_other 6.466 r_dihedral_angle_1_deg 6.026 r_scangle_other 4.74 r_mcangle_other 3.723 r_mcangle_it 3.721 r_scbond_it 2.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.605 r_dihedral_angle_4_deg 18.311 r_dihedral_angle_3_deg 13.492 r_long_range_B_refined 6.534 r_long_range_B_other 6.466 r_dihedral_angle_1_deg 6.026 r_scangle_other 4.74 r_mcangle_other 3.723 r_mcangle_it 3.721 r_scbond_it 2.912 r_scbond_other 2.912 r_mcbond_it 2.499 r_mcbond_other 2.498 r_angle_refined_deg 1.408 r_angle_other_deg 0.968 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5564 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building