4PMY

Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri complexed with xylose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	Polyethylene glycol 8,000

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.866	α = 90
b = 48.201	β = 90.12
c = 77.798	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		2013-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.033	LNLS	W01B-MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.6	50	98.7	0.095	0.112	11.54	3.54		69577		-3	21.057

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.7	96.5		0.589	0.693	2.55

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.601	40.97	69577	3516	98.72	0.1877	0.1856	0.2268	RANDOM	14.034

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]
0.2		0.02	0.16		-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.874
r_sphericity_free	24.714
r_dihedral_angle_4_deg	16.675
r_dihedral_angle_3_deg	12.591
r_sphericity_bonded	12.523
r_dihedral_angle_1_deg	5.033
r_scbond_it	1.853
r_mcangle_it	1.746
r_mcbond_it	1.331
r_angle_refined_deg	1.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.874
r_sphericity_free	24.714
r_dihedral_angle_4_deg	16.675
r_dihedral_angle_3_deg	12.591
r_sphericity_bonded	12.523
r_dihedral_angle_1_deg	5.033
r_scbond_it	1.853
r_mcangle_it	1.746
r_mcbond_it	1.331
r_angle_refined_deg	1.016
r_rigid_bond_restr	0.978
r_chiral_restr	0.074
r_bond_refined_d	0.005
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4840
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	34

Software

Software
Software Name	Purpose
XDS	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.