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Crystal structure of eukaryotic O-GlcNAcase HAT-like domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BMH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M HEPES 7.5, 60 mM Sodium potassium-tartrate and 27.5 % PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.26 45.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.25 α = 87.52 b = 43.52 β = 85.24 c = 59.84 γ = 87.58
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 2M 2014-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.784 59.59 89 0.07 0.99 8 1.6 36731
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 1.784 1.848
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 4BMH 1.784 36.36 35956 775 88.84 0.19351 0.19257 0.2014 0.23979 0.2412 RANDOM 22.125
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] 0.84 -1.5 0.28 0.42 -0.45 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.179 r_dihedral_angle_4_deg 15.988 r_dihedral_angle_3_deg 14.293 r_dihedral_angle_1_deg 7.573 r_long_range_B_refined 5.398 r_long_range_B_other 5.392 r_scangle_other 4.04 r_mcangle_it 2.798 r_mcangle_other 2.797 r_scbond_it 2.566
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.179 r_dihedral_angle_4_deg 15.988 r_dihedral_angle_3_deg 14.293 r_dihedral_angle_1_deg 7.573 r_long_range_B_refined 5.398 r_long_range_B_other 5.392 r_scangle_other 4.04 r_mcangle_it 2.798 r_mcangle_other 2.797 r_scbond_it 2.566 r_scbond_other 2.565 r_mcbond_it 1.887 r_mcbond_other 1.886 r_angle_refined_deg 1.567 r_angle_other_deg 1.396 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 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 3388 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing