5LA0

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 DIFFUSION293.151 M ammonium sulphate, 0.1 M Bis- Tris, 1 % PEG 3350 pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.4549.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.092α = 90
b = 72.366β = 90
c = 109.113γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2011-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9173DiamondI04-1

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
11.6544.8598.50.0670.998133.5635231.5
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)
11.651.6899.40.6511.63.6

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 REPLACEMENTTHROUGHOUT5AK11.6544.8560345312398.230.124590.122210.16975RANDOM19.594
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]
1.37-0.9-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free42.071
r_dihedral_angle_2_deg32.774
r_dihedral_angle_4_deg16.404
r_dihedral_angle_3_deg11.908
r_sphericity_bonded11.037
r_dihedral_angle_1_deg6.247
r_long_range_B_refined5.144
r_long_range_B_other3.742
r_scangle_other2.983
r_scbond_it2.511
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free42.071
r_dihedral_angle_2_deg32.774
r_dihedral_angle_4_deg16.404
r_dihedral_angle_3_deg11.908
r_sphericity_bonded11.037
r_dihedral_angle_1_deg6.247
r_long_range_B_refined5.144
r_long_range_B_other3.742
r_scangle_other2.983
r_scbond_it2.511
r_scbond_other2.511
r_mcangle_other2.211
r_mcangle_it2.209
r_rigid_bond_restr2.002
r_mcbond_it1.732
r_mcbond_other1.722
r_angle_refined_deg1.564
r_angle_other_deg1.022
r_chiral_restr0.102
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.003
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 Atoms3712
Nucleic Acid Atoms
Solvent Atoms579
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction