6FWJ

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5M17 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2923 M sodium acetate, pH 6.4 - 7.4
Crystal Properties
Matthews coefficientSolvent content
2.2745.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.636α = 90
b = 108.636β = 90
c = 67.643γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
11.0476.8298.80.0750.0810.0420.9939.57.518542312.71
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)
11.041.0680.41.3461.4820.6010.4550.85.5

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 REPLACEMENTTHROUGHOUT5M171.0476.82176271915298.710.128560.127610.14653RANDOM16.751
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]
-0.06-0.060.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.634
r_sphericity_free29.355
r_dihedral_angle_4_deg19.774
r_dihedral_angle_3_deg12.467
r_dihedral_angle_1_deg8.397
r_sphericity_bonded7.467
r_long_range_B_refined2.816
r_long_range_B_other2.448
r_rigid_bond_restr2.383
r_scangle_other1.979
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.634
r_sphericity_free29.355
r_dihedral_angle_4_deg19.774
r_dihedral_angle_3_deg12.467
r_dihedral_angle_1_deg8.397
r_sphericity_bonded7.467
r_long_range_B_refined2.816
r_long_range_B_other2.448
r_rigid_bond_restr2.383
r_scangle_other1.979
r_angle_refined_deg1.772
r_scbond_it1.677
r_scbond_other1.677
r_mcangle_it1.515
r_mcangle_other1.514
r_angle_other_deg1.194
r_mcbond_it1.17
r_mcbond_other1.156
r_chiral_restr0.111
r_bond_refined_d0.013
r_gen_planes_refined0.012
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 Atoms2799
Nucleic Acid Atoms
Solvent Atoms381
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing