☰ Navigation Tabs
Screening-based discovery of drug-like O-GlcNAcase inhibitor scaffolds
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CBJ PDB ENTRY 2CBJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE PH 6.5 AND 30 % PEG 8000 AND GAMMA-BUTYROLACTONE
Crystal Properties Matthews coefficient Solvent content 2.76 55.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.405 α = 90 b = 148.549 β = 90 c = 151.97 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 2.25 20 99.9 0.11 14.8 4 71167 2
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 2.25 2.33 99.9 0.43 3 3.9
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 2CBJ 2.25 19.88 68464 1400 99.88 0.20433 0.20348 0.1955 0.2465 0.2412 RANDOM 27.805
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] 0.04 0.15 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.948 r_dihedral_angle_4_deg 17.596 r_dihedral_angle_3_deg 16.949 r_dihedral_angle_1_deg 6.757 r_scangle_it 5.09 r_scbond_it 3.23 r_mcangle_it 1.934 r_angle_refined_deg 1.799 r_mcbond_it 1.044 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.948 r_dihedral_angle_4_deg 17.596 r_dihedral_angle_3_deg 16.949 r_dihedral_angle_1_deg 6.757 r_scangle_it 5.09 r_scbond_it 3.23 r_mcangle_it 1.934 r_angle_refined_deg 1.799 r_mcbond_it 1.044 r_chiral_restr 0.133 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 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 9249 Nucleic Acid Atoms Solvent Atoms 825 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement DENZO data scaling REFMAC phasing