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Complex of a C. perfringens O-GlcNAcase with a fragment hit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 Apo crystals were grown in 0.6 M NaAcetate pH 7.5, 0.175 M cadmium sulphate (ML).
Crystals were then transferred into a drop supplemented with 10 mM ligand and incubated for 4 h. Crystals were cryo-protected by short immersion in ML supplemented with 20% glycerol and saturated with ligand.
Crystal Properties Matthews coefficient Solvent content 4.46 72.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.794 α = 90 b = 117.794 β = 90 c = 147.233 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 4M 2017-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9678 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.6 50.01 99.1 0.222 0.254 0.122 0.993 7.9 7.9 35270
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 99.5 2.38 2.704 0.1273 0.7 1 8.2
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 2YDS 2.6 50.01 33390 1880 99.06 0.17436 0.17174 0.1799 0.22061 0.2239 RANDOM 62.48
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] 2.15 1.07 2.15 -6.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.134 r_dihedral_angle_4_deg 17.58 r_dihedral_angle_3_deg 17.532 r_long_range_B_refined 10.522 r_long_range_B_other 10.522 r_scangle_other 8.657 r_dihedral_angle_1_deg 7.113 r_mcangle_it 6.492 r_mcangle_other 6.491 r_scbond_it 5.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.134 r_dihedral_angle_4_deg 17.58 r_dihedral_angle_3_deg 17.532 r_long_range_B_refined 10.522 r_long_range_B_other 10.522 r_scangle_other 8.657 r_dihedral_angle_1_deg 7.113 r_mcangle_it 6.492 r_mcangle_other 6.491 r_scbond_it 5.691 r_scbond_other 5.69 r_mcbond_it 4.503 r_mcbond_other 4.502 r_angle_refined_deg 1.774 r_angle_other_deg 1.085 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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 4586 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing