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Human O-GlcNAc transferase in complex with a bisubstrate inhibitor, Goblin1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AY6 PDB ENTRY 4AY6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9.3 1.45 M K2HPO4, 10 MM EDTA, 1% XYLITOL, pH 9.3
Crystal Properties Matthews coefficient Solvent content 4.8 74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 273.728 α = 90 b = 273.728 β = 90 c = 142.581 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 PILATUS 6M 2012-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 3.15 30 99.2 0.14 9.2 4.3 104870 2
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 3.15 3.3 99.7 0.5 3.1 4.5
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 PDB ENTRY 4AY6 3.15 30 101727 3141 99.03 0.19746 0.19697 0.1924 0.21338 0.2091 RANDOM 54.631
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] 1.09 0.55 1.09 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.29 r_dihedral_angle_4_deg 18.701 r_dihedral_angle_3_deg 16.806 r_dihedral_angle_1_deg 5.633 r_scangle_it 3.311 r_scbond_it 1.803 r_mcangle_it 1.412 r_angle_refined_deg 1.343 r_mcbond_it 0.704 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.29 r_dihedral_angle_4_deg 18.701 r_dihedral_angle_3_deg 16.806 r_dihedral_angle_1_deg 5.633 r_scangle_it 3.311 r_scbond_it 1.803 r_mcangle_it 1.412 r_angle_refined_deg 1.343 r_mcbond_it 0.704 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22268 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 255
Software Software Software Name Purpose REFMAC refinement xia2 data reduction SCALA data scaling REFMAC phasing