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Structure of human O-GlcNAc hydrolase with bound transition state analog ThiametG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 292 0.1-0.2 M tri ammonium citrate pH 7.5
16-20 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.45 49.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.908 α = 90 b = 101.908 β = 90 c = 282.799 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 PILATUS3 6M 2016-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 96.06 100 0.121 0.035 13.4 12.6 59331
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.47 100 2.857 0.847 0.463 1 11.7
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 (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 2.4 96.06 59286 1770 99.95 0.2078 0.207 0.21 0.2322 0.2307 RANDOM 78.1132
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] -0.22 -0.22 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.415 r_dihedral_angle_4_deg 18.978 r_dihedral_angle_3_deg 18.21 r_dihedral_angle_1_deg 6.411 r_angle_other_deg 3.652 r_mcangle_it 2.169 r_angle_refined_deg 1.609 r_mcbond_it 1.267 r_mcbond_other 1.267 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.415 r_dihedral_angle_4_deg 18.978 r_dihedral_angle_3_deg 18.21 r_dihedral_angle_1_deg 6.411 r_angle_other_deg 3.652 r_mcangle_it 2.169 r_angle_refined_deg 1.609 r_mcbond_it 1.267 r_mcbond_other 1.267 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_other 0.01 r_gen_planes_refined 0.007 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7260 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing