5MC8

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-D-glucal 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 DROP7.42923 M sodium acetate, pH 7.4
Crystal Properties
Matthews coefficientSolvent content
2.2745.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.624α = 90
b = 108.624β = 90
c = 67.692γ = 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
11.1857.4599.70.0520.9989.14.412850912.39
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)
11.181.295.50.790.7060.94

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 4UTF1.1857.45122113639699.680.137140.136070.15749RANDOM17.478
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]
-0.82-0.821.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.185
r_sphericity_free29.731
r_dihedral_angle_4_deg18.91
r_dihedral_angle_3_deg12.595
r_sphericity_bonded10.175
r_dihedral_angle_1_deg8.771
r_long_range_B_refined3.071
r_long_range_B_other2.801
r_scangle_other2.05
r_rigid_bond_restr1.808
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.185
r_sphericity_free29.731
r_dihedral_angle_4_deg18.91
r_dihedral_angle_3_deg12.595
r_sphericity_bonded10.175
r_dihedral_angle_1_deg8.771
r_long_range_B_refined3.071
r_long_range_B_other2.801
r_scangle_other2.05
r_rigid_bond_restr1.808
r_scbond_it1.708
r_scbond_other1.706
r_mcangle_other1.56
r_mcangle_it1.556
r_angle_refined_deg1.458
r_angle_other_deg1.366
r_mcbond_it1.244
r_mcbond_other1.214
r_chiral_restr0.093
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.003
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 Atoms2804
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing