6FWI

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-(1,2-anhydro-carba-mannosamine)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AD4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72923 M sodium acetate, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.2845.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.459α = 90
b = 108.459β = 90
c = 68.034γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2014-10-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

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
11.2576.6999.40.0590.0630.0220.99817.48.210808812.5
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)
11.251.271001.6641.7860.6430.4621.37.6

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 REPLACEMENTTHROUGHOUT4AD41.2576.69102687540099.340.126670.125610.14686RANDOM17.203
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]
-0.79-0.791.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.665
r_sphericity_free26.387
r_dihedral_angle_4_deg17.855
r_dihedral_angle_3_deg12.303
r_sphericity_bonded10.278
r_dihedral_angle_1_deg5.769
r_long_range_B_refined2.882
r_long_range_B_other2.715
r_scangle_other2.229
r_scbond_it1.795
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.665
r_sphericity_free26.387
r_dihedral_angle_4_deg17.855
r_dihedral_angle_3_deg12.303
r_sphericity_bonded10.278
r_dihedral_angle_1_deg5.769
r_long_range_B_refined2.882
r_long_range_B_other2.715
r_scangle_other2.229
r_scbond_it1.795
r_scbond_other1.795
r_mcangle_other1.607
r_mcangle_it1.604
r_angle_refined_deg1.424
r_rigid_bond_restr1.389
r_mcbond_it1.254
r_mcbond_other1.222
r_angle_other_deg1.029
r_chiral_restr0.092
r_bond_refined_d0.009
r_gen_planes_refined0.009
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 Atoms2764
Nucleic Acid Atoms
Solvent Atoms268
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing