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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 5UN8
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 55.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.507 α = 90 b = 96.06 β = 114.51 c = 88.968 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 300 mm CCD 2017-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.978 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 50.01 99.8 0.043 22 4.4 34865
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 97.3 0.41 1.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5UN8 2.7 50 33154 1656 99.82 0.21091 0.20766 0.27549 0.2555 RANDOM 68.302
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] 0.96 1.6 1.81 -2.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.291 r_dihedral_angle_3_deg 17.842 r_dihedral_angle_4_deg 15.643 r_long_range_B_refined 13.408 r_mcangle_it 7.946 r_dihedral_angle_1_deg 6.436 r_scbond_it 6.151 r_mcbond_it 5.243 r_angle_refined_deg 1.592 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.291 r_dihedral_angle_3_deg 17.842 r_dihedral_angle_4_deg 15.643 r_long_range_B_refined 13.408 r_mcangle_it 7.946 r_dihedral_angle_1_deg 6.436 r_scbond_it 6.151 r_mcbond_it 5.243 r_angle_refined_deg 1.592 r_chiral_restr 0.108 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 7062 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing