5LA1

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 Na/K phosphate, 100 mM MES pH 6.5 and 2M NaCl.
Crystal Properties
Matthews coefficientSolvent content
2.4950.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.911α = 90
b = 72.514β = 90
c = 109.537γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-05-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9772DiamondI24

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
11.945.1698.60.0280.99926.63.6427161.5
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)
11.91.94850.08482.1

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 REPLACEMENTTHROUGHOUT5AK11.945.1640566209098.370.130970.129440.16041RANDOM17.065
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]
1.3-0.55-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.878
r_dihedral_angle_4_deg18.325
r_dihedral_angle_3_deg11.452
r_dihedral_angle_1_deg6.199
r_long_range_B_refined5.722
r_long_range_B_other5.722
r_scangle_other2.587
r_mcangle_other1.646
r_mcangle_it1.643
r_scbond_it1.639
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.878
r_dihedral_angle_4_deg18.325
r_dihedral_angle_3_deg11.452
r_dihedral_angle_1_deg6.199
r_long_range_B_refined5.722
r_long_range_B_other5.722
r_scangle_other2.587
r_mcangle_other1.646
r_mcangle_it1.643
r_scbond_it1.639
r_scbond_other1.639
r_angle_refined_deg1.621
r_mcbond_it1.087
r_mcbond_other1.072
r_angle_other_deg0.992
r_chiral_restr0.222
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3704
Nucleic Acid Atoms
Solvent Atoms599
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction