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O-GlcNAc transferase TPR domain with the intellectual disability associated mutation L254F
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W3B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295.2 0.1 M Na-HEPES and 0.1 M MOPS-HCl pH 7,5, 0.04 M diethylene glycol, 0.04 M triethylene glycol, 0.04 M tetraethylene glycol, 0.04 M pentaethylene glycol, 20 % v/v ethylene glycol and 10 % w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45 α = 90 b = 203.162 β = 90 c = 116.87 γ = 90
Symmetry Space Group C 2 2 21
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 EIGER X 4M 2016-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.75 46.58 99.7 0.05 0.06 0.04 1 13 4.1 54404 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 99.8 0.57 0.73 0.45 0.76 2 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 1W3B 1.75 101.58 51770 2582 99.47 0.19268 0.19101 0.2026 0.22681 0.2388 RANDOM 37.879
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] 0.5 0.87 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.935 r_dihedral_angle_4_deg 17.492 r_dihedral_angle_3_deg 14.651 r_long_range_B_refined 10.661 r_long_range_B_other 8.785 r_scangle_other 7.45 r_dihedral_angle_1_deg 6.239 r_scbond_it 4.915 r_scbond_other 4.906 r_mcangle_other 4.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.935 r_dihedral_angle_4_deg 17.492 r_dihedral_angle_3_deg 14.651 r_long_range_B_refined 10.661 r_long_range_B_other 8.785 r_scangle_other 7.45 r_dihedral_angle_1_deg 6.239 r_scbond_it 4.915 r_scbond_other 4.906 r_mcangle_other 4.799 r_mcangle_it 4.787 r_mcbond_it 3.686 r_mcbond_other 3.663 r_angle_refined_deg 2.068 r_angle_other_deg 1.186 r_chiral_restr 0.138 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 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 2692 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing