6FAR

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-mannoimidazole


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
2.2745.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.619α = 90
b = 108.619β = 90
c = 67.766γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.376.8199.50.0540.0570.020.999147.59614715.83
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)
11.31.3292.71.2241.3760.7540.4864.6

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 REPLACEMENTTHROUGHOUT5M171.376.8191334481099.430.135370.133980.16168RANDOM20.958
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]
-0.52-0.521.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.32
r_sphericity_free25.562
r_dihedral_angle_4_deg15.181
r_dihedral_angle_3_deg13.061
r_sphericity_bonded9.515
r_dihedral_angle_1_deg5.813
r_long_range_B_refined3.444
r_long_range_B_other2.972
r_scangle_other2.353
r_scbond_it2.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.32
r_sphericity_free25.562
r_dihedral_angle_4_deg15.181
r_dihedral_angle_3_deg13.061
r_sphericity_bonded9.515
r_dihedral_angle_1_deg5.813
r_long_range_B_refined3.444
r_long_range_B_other2.972
r_scangle_other2.353
r_scbond_it2.008
r_scbond_other2.003
r_rigid_bond_restr1.911
r_mcangle_it1.844
r_mcangle_other1.844
r_mcbond_it1.541
r_angle_refined_deg1.497
r_mcbond_other1.492
r_angle_other_deg1.008
r_chiral_restr0.098
r_bond_refined_d0.011
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 Atoms2800
Nucleic Acid Atoms
Solvent Atoms425
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing