2DDX | pdb_00002ddx

Crystal structure of beta-1,3-xylanase from Vibrio sp. AX-4

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.5	293	1M sodium citrate, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2	VAPOR DIFFUSION, HANGING DROP	9.5	293	1M sodium citrate, 0.1M CHES, 20% glycerol, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.873	α = 90
b = 75.654	β = 90
c = 82.119	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 QUANTUM 210		2003-12-21	M	MAD
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2004-04-27	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	0.974, 0.978, 0.960	Photon Factory	AR-NW12A
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	0.900	Photon Factory	BL-5A

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	0.86	50	96.9	0.075	11.4	7	272709	264110		5

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	0.86	0.89	74.7		0.503		2.9	20202

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	0.86	19.85	250801	13309	96.85	0.13988	0.13946	0.149	0.14772	0.1563	RANDOM	6.847

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]
-0.01			0.02		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.891
r_dihedral_angle_4_deg	13.85
r_dihedral_angle_3_deg	10.976
r_dihedral_angle_1_deg	5.746
r_sphericity_free	2.226
r_sphericity_bonded	1.857
r_scangle_it	1.683
r_scbond_it	1.281
r_angle_refined_deg	1.185
r_mcangle_it	0.928
r_rigid_bond_restr	0.9
r_angle_other_deg	0.816
r_mcbond_it	0.727
r_symmetry_vdw_refined	0.586
r_mcbond_other	0.286
r_nbd_refined	0.201
r_symmetry_vdw_other	0.194
r_nbtor_refined	0.183
r_nbd_other	0.178
r_symmetry_hbond_refined	0.115
r_xyhbond_nbd_refined	0.091
r_nbtor_other	0.087
r_chiral_restr	0.073
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2540
Nucleic Acid Atoms
Solvent Atoms	404
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing