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Human O-GlcNAc hydrolase in complex with DNJNAc-thiazolidines
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, HANGING DROP 7.5 291.15 0.14 - 0.2 M triammonium citrate pH 7.5, 16-20 % PEG 3350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.288 α = 90 b = 101.288 β = 90 c = 284.519 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 16M 2018-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.41 58.278 100 0.054 0.056 0.014 1 26.5 15.8 58274
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 2.41 2.48 2.28 2.356 0.59 0.563 1.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5M7R 2.41 58.278 58168 1735 99.921 0.222 0.2205 0.2192 0.2714 0.2705 79.395
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] -1.676 -1.676 3.351
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.071 r_dihedral_angle_4_deg 17.438 r_dihedral_angle_3_deg 16.874 r_lrange_it 12.484 r_lrange_other 12.484 r_mcangle_it 10.288 r_mcangle_other 10.287 r_scangle_it 9.852 r_scangle_other 9.852 r_mcbond_it 7.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.071 r_dihedral_angle_4_deg 17.438 r_dihedral_angle_3_deg 16.874 r_lrange_it 12.484 r_lrange_other 12.484 r_mcangle_it 10.288 r_mcangle_other 10.287 r_scangle_it 9.852 r_scangle_other 9.852 r_mcbond_it 7.3 r_mcbond_other 7.3 r_dihedral_angle_1_deg 7.283 r_scbond_it 7.002 r_scbond_other 7.001 r_angle_refined_deg 1.534 r_angle_other_deg 1.252 r_nbd_refined 0.217 r_nbd_other 0.21 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.158 r_symmetry_nbd_refined 0.12 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.048 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 6704 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing