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GlcNAcstatins are nanomolar inhibitors of human O-GlcNAcase inducing cellular hyper-O-GlcNAcylation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J62 PDB ENTRY 2J62
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 30% PEG 8000, 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM COCADYLATE, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.817 α = 90 b = 145.723 β = 90 c = 152.331 γ = 90
Symmetry Space Group I 21 21 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 CCD ADSC CCD 2008-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.3 29.95 98.2 0.07 12.1 3.7 62941 1.8
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 2.3 2.38 95.1 0.57 1.8 3.1
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 PDB ENTRY 2J62 2.31 29.95 59800 600 100 0.18683 0.18635 0.1837 0.23691 0.2315 RANDOM 31.808
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] -0.06 0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.985 r_dihedral_angle_3_deg 17.571 r_dihedral_angle_4_deg 16.992 r_dihedral_angle_1_deg 6.829 r_scangle_it 3.183 r_scbond_it 2.019 r_angle_refined_deg 1.473 r_mcangle_it 1.105 r_mcbond_it 0.588 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.985 r_dihedral_angle_3_deg 17.571 r_dihedral_angle_4_deg 16.992 r_dihedral_angle_1_deg 6.829 r_scangle_it 3.183 r_scbond_it 2.019 r_angle_refined_deg 1.473 r_mcangle_it 1.105 r_mcbond_it 0.588 r_chiral_restr 0.099 r_bond_refined_d 0.014 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_other r_long_range_B_refined 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 9254 Nucleic Acid Atoms Solvent Atoms 641 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing