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Crystal structure of human O-GlcNAcase in complex with an S-linked CKII peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M7R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.14 - 0.2 M triammonium citrate pH 7.5, 16-20 % PEG 3350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.499 α = 90 b = 101.499 β = 90 c = 284.617 γ = 90
Symmetry Space Group P 43 21 2
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 EIGER2 XE 9M 2018-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 2.5 284.62 100 0.101 0.108 0.037 0.999 14.4 15.7 52629
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 2.5 2.58 0.84 0.892 0.3 0.843 16.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 95.785 52525 1571 99.964 0.218 0.2158 0.216 0.2711 0.271 68.096
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] -4.059 -4.059 8.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.029 r_dihedral_angle_6_deg 16.378 r_lrange_other 11.633 r_lrange_it 11.632 r_dihedral_angle_2_deg 11.39 r_mcangle_it 10.176 r_mcangle_other 10.175 r_scangle_it 8.962 r_scangle_other 8.962 r_dihedral_angle_1_deg 7.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.029 r_dihedral_angle_6_deg 16.378 r_lrange_other 11.633 r_lrange_it 11.632 r_dihedral_angle_2_deg 11.39 r_mcangle_it 10.176 r_mcangle_other 10.175 r_scangle_it 8.962 r_scangle_other 8.962 r_dihedral_angle_1_deg 7.496 r_mcbond_it 6.952 r_mcbond_other 6.948 r_scbond_it 6.343 r_scbond_other 6.342 r_angle_refined_deg 1.446 r_symmetry_xyhbond_nbd_refined 0.566 r_angle_other_deg 0.504 r_nbd_other 0.282 r_nbd_refined 0.241 r_symmetry_nbd_other 0.209 r_nbtor_refined 0.196 r_xyhbond_nbd_refined 0.163 r_symmetry_xyhbond_nbd_other 0.117 r_dihedral_angle_other_3_deg 0.086 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.066 r_chiral_restr_other 0.044 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6955 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement Aimless data scaling