5M3W

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4UTFmodified 4UTF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72923 M sodium acetate, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.2645.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.4α = 90
b = 108.4β = 90
c = 67.587γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979DiamondI02

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
11.0476.65990.0520.99413618468812.05
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.041.0687.31.0630.42713.5

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 REPLACEMENTTHROUGHOUTmodified 4UTF1.0476.65175534915198.980.119340.118630.13299RANDOM16.113
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]
-0.26-0.260.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.083
r_sphericity_free30.272
r_dihedral_angle_4_deg19.243
r_dihedral_angle_3_deg12.449
r_dihedral_angle_1_deg8.189
r_sphericity_bonded7.644
r_long_range_B_refined3.122
r_long_range_B_other2.637
r_scangle_other1.896
r_rigid_bond_restr1.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.083
r_sphericity_free30.272
r_dihedral_angle_4_deg19.243
r_dihedral_angle_3_deg12.449
r_dihedral_angle_1_deg8.189
r_sphericity_bonded7.644
r_long_range_B_refined3.122
r_long_range_B_other2.637
r_scangle_other1.896
r_rigid_bond_restr1.77
r_angle_refined_deg1.609
r_scbond_it1.558
r_scbond_other1.554
r_mcangle_other1.408
r_mcangle_it1.404
r_angle_other_deg1.089
r_mcbond_it1.025
r_mcbond_other1.002
r_chiral_restr0.102
r_bond_refined_d0.011
r_gen_planes_refined0.011
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2822
Nucleic Acid Atoms
Solvent Atoms368
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing