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Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase
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 EVAPORATION 293 0.08 M BIS-TRIS propane (pH 7.0), 0.02 M sodium cacodylate trihydrate (pH 6.5), 2.8 M sodium formate, 0.04 M ammonium sulfate, and 6% w/v polyethylene glycol 8,000.
Crystal Properties Matthews coefficient Solvent content 3.38 63.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.084 α = 90 b = 152.733 β = 90 c = 199.398 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 293 CCD MARMOSAIC 300 mm CCD 2015-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.978 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.1 50.01 99.6 0.073 0.031 40.8 6.7 58556
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 2.13 2.17 98.3 0.36 0.157 0.963 4 6
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 3PE3 2.25 50.01 47541 2558 99.69 0.18424 0.18175 0.1849 0.22849 0.2314 RANDOM 53.82
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] -2.55 6.56 -4.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.783 r_dihedral_angle_4_deg 19.152 r_dihedral_angle_3_deg 16.938 r_long_range_B_refined 11.856 r_mcangle_it 7.023 r_scbond_it 7.009 r_dihedral_angle_1_deg 6.719 r_mcbond_it 5.097 r_angle_refined_deg 2.052 r_chiral_restr 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.783 r_dihedral_angle_4_deg 19.152 r_dihedral_angle_3_deg 16.938 r_long_range_B_refined 11.856 r_mcangle_it 7.023 r_scbond_it 7.009 r_dihedral_angle_1_deg 6.719 r_mcbond_it 5.097 r_angle_refined_deg 2.052 r_chiral_restr 0.141 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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_it r_scangle_other 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 5481 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing