5LA2

The mechanism by which arabinoxylanases can recognise highly decorated xylans

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5AK1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293.15	100 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 coefficient	Solvent content
2.72	54.79

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2015-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9791	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.65	48.43	99.8	0.057	0.988	11.2	3.3		140288		1.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	99.4		0.749	1.6	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5AK1	1.65	48.43	133265	6940	98.6	0.14901	0.14637	0.19855	RANDOM	21.695

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]
-0.59			0.7		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	34.455
r_dihedral_angle_2_deg	33.549
r_dihedral_angle_4_deg	16.097
r_dihedral_angle_3_deg	11.761
r_sphericity_bonded	9.352
r_dihedral_angle_1_deg	6.39
r_long_range_B_refined	4.771
r_long_range_B_other	3.891
r_scangle_other	2.94
r_mcangle_other	2.596
r_mcangle_it	2.594
r_scbond_it	2.583
r_scbond_other	2.579
r_mcbond_it	2.178
r_mcbond_other	2.175
r_rigid_bond_restr	2.081
r_angle_refined_deg	1.533
r_angle_other_deg	0.972
r_chiral_restr	0.091
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	7241
Nucleic Acid Atoms
Solvent Atoms	923
Heterogen Atoms	118

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
XDS	data reduction
XDS	data scaling