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The human O-GlcNAc transferase in complex with a bisubstrate inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 295 1.3 M DL-Malic acid, 0.1 M Bis-Tris propane pH 6.4 + seeds generated out of this condition
Crystal Properties Matthews coefficient Solvent content 3.34 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.869 α = 90 b = 151.333 β = 90 c = 200.478 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 PILATUS3 2M 2016-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.98 ESRF MASSIF-1
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 1.68 46.1 99.3 0.05 0.06 0.04 0.99 13 4.7 117257
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 1.68 1.71 99.9 1.285 1.624 0.979 0.45 1 4.8
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 THROUGHOUT 1.68 46.1 111305 5933 99.18 0.1942 0.19277 0.2027 0.22143 0.2297 RANDOM 36.148
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] -0.49 2.13 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.992 r_dihedral_angle_4_deg 17.367 r_dihedral_angle_3_deg 12.546 r_dihedral_angle_1_deg 5.416 r_long_range_B_refined 5.377 r_long_range_B_other 5.251 r_scangle_other 3.371 r_mcangle_other 2.518 r_mcangle_it 2.517 r_scbond_it 2.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.992 r_dihedral_angle_4_deg 17.367 r_dihedral_angle_3_deg 12.546 r_dihedral_angle_1_deg 5.416 r_long_range_B_refined 5.377 r_long_range_B_other 5.251 r_scangle_other 3.371 r_mcangle_other 2.518 r_mcangle_it 2.517 r_scbond_it 2.006 r_scbond_other 2.006 r_mcbond_it 1.586 r_mcbond_other 1.585 r_angle_refined_deg 1.244 r_angle_other_deg 0.925 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 5475 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building