6HMH

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-(1,2-anhydro-carba-glucosamine) 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 DROP7.42923 M sodium acetate, pH 7.4
Crystal Properties
Matthews coefficientSolvent content
2.2545.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.175α = 90
b = 108.175β = 90
c = 67.575γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-02-19MSINGLE 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)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
11.0357.31980.0580.0650.0280.98812.46.118783212.66
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)
11.031.0575.81.2381.4230.6790.40913.8

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 REPLACEMENTTHROUGHOUT5M171.0357.311785249303980.124840.124080.13935RANDOM16.585
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]
-0.28-0.280.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.328
r_sphericity_free24.764
r_dihedral_angle_4_deg18.352
r_dihedral_angle_3_deg12.859
r_sphericity_bonded9.043
r_dihedral_angle_1_deg5.982
r_long_range_B_refined3.805
r_long_range_B_other2.52
r_rigid_bond_restr2.047
r_scangle_other1.874
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.328
r_sphericity_free24.764
r_dihedral_angle_4_deg18.352
r_dihedral_angle_3_deg12.859
r_sphericity_bonded9.043
r_dihedral_angle_1_deg5.982
r_long_range_B_refined3.805
r_long_range_B_other2.52
r_rigid_bond_restr2.047
r_scangle_other1.874
r_angle_refined_deg1.609
r_scbond_it1.592
r_scbond_other1.592
r_mcangle_other1.458
r_mcangle_it1.454
r_mcbond_it1.149
r_mcbond_other1.138
r_angle_other_deg1.073
r_chiral_restr0.108
r_bond_refined_d0.012
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 Atoms2764
Nucleic Acid Atoms
Solvent Atoms381
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing