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Structural Investigations of the Substrate Specificity of Human O-GlcNAcase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 293 0.024 M ammonium citrate tribasic (pH 7.0), 0.015 M MES monohydrate, 0.096 M potassium thiocyanate, 0.25 M Sodium acetate trihydrate, 0.037 M imidazole, 0.002 M zinc sulfate heptahydrate, 9.6 % w/v polyethylene glycol 3,350, 2.4 % w/v polyethylene glycol monomethyl ether 2,000, and 4% w/v polyethylene glycol monomethyl ether 550
Crystal Properties Matthews coefficient Solvent content 2.74 55.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.922 α = 90 b = 96.222 β = 114.56 c = 89.653 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD MARMOSAIC 225 mm CCD 2017-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.978 APS 21-ID-F
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 2.9 50 99.8 0.089 20.4 4.6 28990
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 2.9 2.95 98.9 0.69 1.8 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 5TKE 2.9 50 26597 1341 96.37 0.20382 0.19988 0.2027 0.28221 0.2761 RANDOM 88.838
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] -0.08 -0.04 0.05 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.347 r_dihedral_angle_3_deg 17.928 r_dihedral_angle_4_deg 14.942 r_long_range_B_other 12.082 r_long_range_B_refined 12.079 r_mcangle_it 9.386 r_mcangle_other 9.385 r_scangle_other 8.671 r_dihedral_angle_1_deg 6.791 r_mcbond_it 6.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.347 r_dihedral_angle_3_deg 17.928 r_dihedral_angle_4_deg 14.942 r_long_range_B_other 12.082 r_long_range_B_refined 12.079 r_mcangle_it 9.386 r_mcangle_other 9.385 r_scangle_other 8.671 r_dihedral_angle_1_deg 6.791 r_mcbond_it 6.153 r_mcbond_other 6.153 r_scbond_it 5.629 r_scbond_other 5.629 r_angle_refined_deg 1.535 r_angle_other_deg 1.017 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 7063 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing