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Crystal structure of the core catalytic domain of human O-GlcNAcase bound to MK-8719
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M K-Na-tartrate tetrahydrate, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.12 60.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.92 α = 77.27 b = 91.46 β = 62.61 c = 94.61 γ = 62.86
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 PILATUS 6M 2011-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.86 70.484 95.1 7.2 1.8 52089 79.71
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.86 2.913
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 FOURIER SYNTHESIS THROUGHOUT 2.86 40.69 52075 2706 95.1 0.243 0.239 0.2508 0.309 0.3201 RANDOM 60.57
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] -3.2021 -6.917 12.1011 6.3583 10.7345 -3.1562
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.29 t_omega_torsion 1.92 t_angle_deg 1.18 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.29 t_omega_torsion 1.92 t_angle_deg 1.18 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13813 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 68
Software Software Software Name Purpose Aimless data scaling BUSTER refinement PDB_EXTRACT data extraction XDS data reduction BUSTER phasing