2J4G

Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with n-butyl- thiazoline inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CHOPDB ENTRY 2CHO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
160.4M SODIUM ACETATE,13%(V/V)PEG 3500, 0.1M MES PH6.0, 10% (V/V) GLYCEROL, pH 6.00
Crystal Properties
Matthews coefficientSolvent content
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 185.106α = 90
b = 51.711β = 100.11
c = 172.782γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.25401000.09184.577267
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)
12.252.331000.4734.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2CHO2.25169.0373055387099.60.2230.220.284RANDOM30.56
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]
0.08-1.79-1.170.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.667
r_dihedral_angle_4_deg18.021
r_dihedral_angle_3_deg16.627
r_dihedral_angle_1_deg10.995
r_scangle_it2.882
r_scbond_it1.932
r_angle_refined_deg1.588
r_mcangle_it1.345
r_mcbond_it0.788
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.667
r_dihedral_angle_4_deg18.021
r_dihedral_angle_3_deg16.627
r_dihedral_angle_1_deg10.995
r_scangle_it2.882
r_scbond_it1.932
r_angle_refined_deg1.588
r_mcangle_it1.345
r_mcbond_it0.788
r_nbtor_refined0.307
r_symmetry_hbond_refined0.23
r_symmetry_vdw_refined0.207
r_nbd_refined0.206
r_xyhbond_nbd_refined0.157
r_chiral_restr0.118
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9457
Nucleic Acid Atoms
Solvent Atoms558
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing