6FAM

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-2-aminodeoxymannojirimycin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42923M sodium acetate, pH 7.4
Crystal Properties
Matthews coefficientSolvent content
2.4549.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.101α = 90
b = 108.101β = 90
c = 67.507γ = 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
11.1376.4499.10.0690.0750.0260.99910.27.514355913.59
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)
11.131.15861.5011.6820.7350.414.8

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 REPLACEMENTTHROUGHOUT5M171.1376.44136411713399.020.123320.122220.14411RANDOM17.888
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]
-0.31-0.310.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.362
r_sphericity_free28.34
r_dihedral_angle_4_deg18.072
r_dihedral_angle_3_deg12.507
r_sphericity_bonded8.362
r_dihedral_angle_1_deg5.918
r_long_range_B_refined3.128
r_long_range_B_other2.64
r_scangle_other1.995
r_mcangle_other1.646
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.362
r_sphericity_free28.34
r_dihedral_angle_4_deg18.072
r_dihedral_angle_3_deg12.507
r_sphericity_bonded8.362
r_dihedral_angle_1_deg5.918
r_long_range_B_refined3.128
r_long_range_B_other2.64
r_scangle_other1.995
r_mcangle_other1.646
r_mcangle_it1.642
r_scbond_it1.611
r_scbond_other1.61
r_angle_refined_deg1.495
r_rigid_bond_restr1.483
r_mcbond_it1.276
r_mcbond_other1.269
r_angle_other_deg1.026
r_chiral_restr0.098
r_bond_refined_d0.01
r_gen_planes_refined0.01
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 Atoms2829
Nucleic Acid Atoms
Solvent Atoms463
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing