6F90

Structure of the family GH92 alpha-mannosidase BT3130 from Bacteroides thetaiotaomicron in complex with Mannoimidazole (ManI)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WVY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.429218% (w/v) PEG 3350, 0.1 M Bis-Tris propane, pH 6.4, 0.2 M NaBr
Crystal Properties
Matthews coefficientSolvent content
4.2370.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 273.666α = 90
b = 273.666β = 90
c = 189.759γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9795DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.449.3899.50.1950.2030.0560.99918.425.116065640.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4499.22.482.580.7020.6611.925.9

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 REPLACEMENTTHROUGHOUT2WVY2.449.38152705794999.350.208950.207220.24227RANDOM62.755
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]
1.060.531.06-3.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.113
r_dihedral_angle_4_deg17.267
r_dihedral_angle_3_deg13.961
r_long_range_B_refined7.526
r_long_range_B_other7.46
r_dihedral_angle_1_deg6.499
r_mcangle_it4.91
r_mcangle_other4.91
r_scangle_other4.175
r_mcbond_it3.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.113
r_dihedral_angle_4_deg17.267
r_dihedral_angle_3_deg13.961
r_long_range_B_refined7.526
r_long_range_B_other7.46
r_dihedral_angle_1_deg6.499
r_mcangle_it4.91
r_mcangle_other4.91
r_scangle_other4.175
r_mcbond_it3.084
r_mcbond_other3.078
r_scbond_it2.563
r_scbond_other2.563
r_angle_refined_deg1.267
r_angle_other_deg0.949
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms16403
Nucleic Acid Atoms
Solvent Atoms1185
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing