6R45

Crystal structure of eukaryotic O-GlcNAcase HAT-like domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.1 M HEPES 7.5, 60 mM Sodium potassium-tartrate and 27.5 % PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.2645.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.25α = 87.52
b = 43.52β = 85.24
c = 59.84γ = 87.58
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2014-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.965ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.78459.59890.070.9981.636731
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.7841.848

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4BMH1.78436.363595677588.840.193510.192570.23979RANDOM22.125
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]
0.84-1.50.280.42-0.45-1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.179
r_dihedral_angle_4_deg15.988
r_dihedral_angle_3_deg14.293
r_dihedral_angle_1_deg7.573
r_long_range_B_refined5.398
r_long_range_B_other5.392
r_scangle_other4.04
r_mcangle_it2.798
r_mcangle_other2.797
r_scbond_it2.566
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.179
r_dihedral_angle_4_deg15.988
r_dihedral_angle_3_deg14.293
r_dihedral_angle_1_deg7.573
r_long_range_B_refined5.398
r_long_range_B_other5.392
r_scangle_other4.04
r_mcangle_it2.798
r_mcangle_other2.797
r_scbond_it2.566
r_scbond_other2.565
r_mcbond_it1.887
r_mcbond_other1.886
r_angle_refined_deg1.567
r_angle_other_deg1.396
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms3388
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing