4PMU

Crystal structure of a novel reducing-end xylose-releasing exo-oligoxylanase (XynA) belonging to GH10 family (space group P1211)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CNC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	Polyethylene glycol 6000

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.022	α = 90
b = 100.741	β = 95.15
c = 134.199	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 225 mm CCD		2013-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.45	LNLS	W01B-MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.857	50	97.7	0.15	5.8	2.9		52305

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	2.857	2.92	95.9		0.61		2.6	2589

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	2CNC	2.857	41.15	52253	2651	97.17	0.2133	0.2107	0.261	RANDOM	45.864

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]
0.43		-0.33	-0.75		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.515
r_dihedral_angle_4_deg	18.849
r_dihedral_angle_3_deg	15.284
r_dihedral_angle_1_deg	5.045
r_mcangle_it	1.105
r_angle_refined_deg	0.944
r_mcbond_it	0.629
r_scbond_it	0.618
r_chiral_restr	0.066
r_bond_refined_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.515
r_dihedral_angle_4_deg	18.849
r_dihedral_angle_3_deg	15.284
r_dihedral_angle_1_deg	5.045
r_mcangle_it	1.105
r_angle_refined_deg	0.944
r_mcbond_it	0.629
r_scbond_it	0.618
r_chiral_restr	0.066
r_bond_refined_d	0.005
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16837
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.