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CpOGA D298N in complex with hOGA-derived S-GlcNAc peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YDQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1:1 drops of proytein mixed with crystallisation buffer: 0.175 M CdSO4 and 0.6 M NaAc
Crystal Properties Matthews coefficient Solvent content 4.52 72.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.651 α = 90 b = 117.651 β = 90 c = 147.9 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 PILATUS3 S 6M 2018-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9686 ESRF ID29
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 3.1 48.17 94.1 0.09 8 3.2 19800
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 3.1 3.31 95.5 0.72 1.5 3.2
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 2YDQ 3.1 48.17 18829 971 93.9 0.19133 0.18925 0.1949 0.23339 0.2279 RANDOM 77.536
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] 1.98 0.99 1.98 -6.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.994 r_dihedral_angle_4_deg 19.615 r_dihedral_angle_3_deg 16.768 r_long_range_B_other 14.842 r_long_range_B_refined 14.841 r_scangle_other 11.369 r_mcangle_other 8.906 r_mcangle_it 8.905 r_scbond_it 7.53 r_scbond_other 7.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.994 r_dihedral_angle_4_deg 19.615 r_dihedral_angle_3_deg 16.768 r_long_range_B_other 14.842 r_long_range_B_refined 14.841 r_scangle_other 11.369 r_mcangle_other 8.906 r_mcangle_it 8.905 r_scbond_it 7.53 r_scbond_other 7.529 r_mcbond_it 6.184 r_mcbond_other 6.177 r_dihedral_angle_1_deg 5.964 r_angle_refined_deg 1.666 r_angle_other_deg 1.608 r_chiral_restr 0.11 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 4594 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing