5LA2

The mechanism by which arabinoxylanases can recognise highly decorated xylans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5AK1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION293.15100 mM Tris-Bicine buffer pH 8.5, 12.5% (w/v) polyethylene glycol average Mw 1,000 Da, 12.5% (w/v) polyethylene glycol average Mw 3,350 Da and 12.5% (RS)-2-methyl-2,4-pentanediol (racemic).
Crystal Properties
Matthews coefficientSolvent content
2.7254.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.273α = 90
b = 123.176β = 90
c = 125.38γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9791DiamondI02

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
11.6548.4399.80.0570.98811.23.31402881.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6899.40.7491.63.4

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 REPLACEMENTTHROUGHOUT5AK11.6548.43133265694098.60.149010.146370.19855RANDOM21.695
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]
-0.590.7-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free34.455
r_dihedral_angle_2_deg33.549
r_dihedral_angle_4_deg16.097
r_dihedral_angle_3_deg11.761
r_sphericity_bonded9.352
r_dihedral_angle_1_deg6.39
r_long_range_B_refined4.771
r_long_range_B_other3.891
r_scangle_other2.94
r_mcangle_other2.596
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free34.455
r_dihedral_angle_2_deg33.549
r_dihedral_angle_4_deg16.097
r_dihedral_angle_3_deg11.761
r_sphericity_bonded9.352
r_dihedral_angle_1_deg6.39
r_long_range_B_refined4.771
r_long_range_B_other3.891
r_scangle_other2.94
r_mcangle_other2.596
r_mcangle_it2.594
r_scbond_it2.583
r_scbond_other2.579
r_mcbond_it2.178
r_mcbond_other2.175
r_rigid_bond_restr2.081
r_angle_refined_deg1.533
r_angle_other_deg0.972
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms7241
Nucleic Acid Atoms
Solvent Atoms923
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
XDSdata scaling