2DRS

Crystal structure of reducing-end-xylose releasing exo-oligoxylanase D263S mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WU4	PDB ENTRY 1WU4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	PEG4000, SODIUM ACETATE, GLYCEROL, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.249	α = 90
b = 85.026	β = 90
c = 86.822	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	CCD	ADSC QUAMTUM 4r		2004-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A	1.0	Photon Factory	BL-6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.1	60.746	97.3	0.099	15.2	4.5	23314	22673			12.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	99.2		0.243	5.9	4.5	2294

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1WU4	2.1	43.4	21506	21506	1163	97.3	0.1437	0.1437	0.14013	0.21041	RANDOM	10.255

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]
-0.02			0.03		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.678
r_dihedral_angle_4_deg	15.409
r_dihedral_angle_3_deg	15.048
r_dihedral_angle_1_deg	6.018
r_scangle_it	3.391
r_scbond_it	2.252
r_angle_refined_deg	1.406
r_mcangle_it	1.367
r_mcbond_it	0.848
r_nbtor_refined	0.313
r_nbd_refined	0.205
r_symmetry_hbond_refined	0.203
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.186
r_chiral_restr	0.106
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3106
Nucleic Acid Atoms
Solvent Atoms	431
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data scaling