6FWL

Structure of an E333Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex alpha-Glc-1,3-(1,2-anhydro-carba-mannose)


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
2.2545.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.233α = 90
b = 108.233β = 90
c = 67.446γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-08-06MSINGLE 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
11.1276.531000.0630.0690.0270.9999.86.414903812.79
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)
11.121.1499.21.3871.5280.8340.451.15.7

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 REPLACEMENTTHROUGHOUT5M171.1276.53141622739899.910.126570.125550.14589RANDOM17.07
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]
-0.05-0.050.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.335
r_sphericity_free26.908
r_dihedral_angle_4_deg19.833
r_dihedral_angle_3_deg12.252
r_dihedral_angle_1_deg8.981
r_sphericity_bonded7.475
r_long_range_B_refined2.927
r_long_range_B_other2.547
r_scangle_other1.952
r_rigid_bond_restr1.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.335
r_sphericity_free26.908
r_dihedral_angle_4_deg19.833
r_dihedral_angle_3_deg12.252
r_dihedral_angle_1_deg8.981
r_sphericity_bonded7.475
r_long_range_B_refined2.927
r_long_range_B_other2.547
r_scangle_other1.952
r_rigid_bond_restr1.76
r_scbond_it1.623
r_scbond_other1.622
r_mcangle_other1.575
r_mcangle_it1.572
r_angle_refined_deg1.557
r_mcbond_it1.211
r_mcbond_other1.206
r_angle_other_deg1.09
r_chiral_restr0.101
r_bond_refined_d0.011
r_gen_planes_refined0.011
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 Atoms2818
Nucleic Acid Atoms
Solvent Atoms405
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing