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Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.45 M K2HPO4, 8 mM EDTA and 1% xylitol
Crystal Properties Matthews coefficient Solvent content 3.17 61.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.737 α = 90 b = 150.617 β = 90 c = 199.996 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 80 PIXEL DECTRIS PILATUS 6M 2018-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.99187 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 100 100 11.3 5.2 286887
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.23 99 0.91 0.848 1.3 5.3
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 5C1D 2.17 100 51399 2677 98.66 0.2035 0.20086 0.2073 0.25368 0.2543 RANDOM 54.861
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] -1.93 4.7 -2.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.025 r_dihedral_angle_4_deg 20.378 r_dihedral_angle_3_deg 15.798 r_long_range_B_refined 9.782 r_long_range_B_other 9.763 r_scangle_other 7.685 r_dihedral_angle_1_deg 6.939 r_mcangle_it 6.76 r_mcangle_other 6.76 r_scbond_it 5.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.025 r_dihedral_angle_4_deg 20.378 r_dihedral_angle_3_deg 15.798 r_long_range_B_refined 9.782 r_long_range_B_other 9.763 r_scangle_other 7.685 r_dihedral_angle_1_deg 6.939 r_mcangle_it 6.76 r_mcangle_other 6.76 r_scbond_it 5.296 r_scbond_other 5.169 r_mcbond_it 4.955 r_mcbond_other 4.954 r_angle_refined_deg 1.781 r_angle_other_deg 1.06 r_chiral_restr 0.098 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 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 5528 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing