5VVO

Structural Investigations of the Substrate Specificity of Human O-GlcNAcase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TKE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION2930.024 M ammonium citrate tribasic (pH 7.0), 0.015 M MES monohydrate, 0.096 M potassium thiocyanate, 0.25 M Sodium acetate trihydrate, 0.037 M imidazole, 0.002 M zinc sulfate heptahydrate, 9.6 % w/v polyethylene glycol 3,350, 2.4 % w/v polyethylene glycol monomethyl ether 2,000, and 4% w/v polyethylene glycol monomethyl ether 550
Crystal Properties
Matthews coefficientSolvent content
2.7855.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.404α = 90
b = 96.83β = 115.24
c = 89.075γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDMARMOSAIC 225 mm CCD2017-03-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.978APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.680.5799.30.08421.96.338896
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6493.30.63125.7

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 REPLACEMENTTHROUGHOUT5TKE2.680.5736678187899.130.215280.213070.25873RANDOM59.102
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]
0.05-0.01-0.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.475
r_dihedral_angle_3_deg16.973
r_dihedral_angle_4_deg16.549
r_long_range_B_refined9.88
r_long_range_B_other9.871
r_scangle_other7.009
r_dihedral_angle_1_deg6.695
r_mcangle_it6.669
r_mcangle_other6.669
r_scbond_it4.519
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.475
r_dihedral_angle_3_deg16.973
r_dihedral_angle_4_deg16.549
r_long_range_B_refined9.88
r_long_range_B_other9.871
r_scangle_other7.009
r_dihedral_angle_1_deg6.695
r_mcangle_it6.669
r_mcangle_other6.669
r_scbond_it4.519
r_scbond_other4.519
r_mcbond_it4.442
r_mcbond_other4.421
r_angle_refined_deg1.62
r_angle_other_deg1.01
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms7089
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing