4UTF

Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-isofagomine and alpha- 1,2-mannobiose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherPREVIOUSLY SOLVED NATIVE APO STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.62.8 M SODIUM ACETATE, PH 6.6
Crystal Properties
Matthews coefficientSolvent content
2.244.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.469α = 90
b = 108.469β = 90
c = 67.755γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.339.41000.0418.86.696371-3.7
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)
11.31.321000.931.86.5

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 REPLACEMENTTHROUGHOUTPREVIOUSLY SOLVED NATIVE APO STRUCTURE1.376.791564479799.960.113330.111960.13901RANDOM19.787
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]
0.140.14-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.562
r_dihedral_angle_2_deg36.055
r_dihedral_angle_4_deg15.771
r_dihedral_angle_3_deg13.299
r_sphericity_bonded9.582
r_dihedral_angle_1_deg6.303
r_mcangle_it2.7
r_scangle_it2.656
r_rigid_bond_restr2.423
r_scbond_it2.375
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.562
r_dihedral_angle_2_deg36.055
r_dihedral_angle_4_deg15.771
r_dihedral_angle_3_deg13.299
r_sphericity_bonded9.582
r_dihedral_angle_1_deg6.303
r_mcangle_it2.7
r_scangle_it2.656
r_rigid_bond_restr2.423
r_scbond_it2.375
r_mcbond_it2.146
r_mcbond_other2.146
r_angle_refined_deg1.517
r_angle_other_deg1.221
r_symmetry_vdw_refined0.354
r_nbd_refined0.251
r_symmetry_vdw_other0.2
r_nbd_other0.19
r_nbtor_refined0.189
r_symmetry_hbond_refined0.152
r_xyhbond_nbd_refined0.119
r_chiral_restr0.093
r_xyhbond_nbd_other0.086
r_nbtor_other0.085
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2815
Nucleic Acid Atoms
Solvent Atoms497
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing