4PMX

Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri in the native form

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
2.16	43.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.463	α = 90
b = 71.834	β = 90
c = 83.839	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	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	1.03	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	1.3	50	94.4	0.04	13.5	2.9		69082

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	1.3	1.32	95.5		0.561		3	3442

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	SAD	THROUGHOUT	1.304	41.95	68887	1873	93.68	0.1333	0.1322	0.1743	RANDOM	14.16

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]
-0.08			0.06		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	35.407
r_dihedral_angle_2_deg	33.682
r_dihedral_angle_4_deg	19.021
r_dihedral_angle_3_deg	11.724
r_sphericity_bonded	10.625
r_dihedral_angle_1_deg	5.948
r_rigid_bond_restr	5.935
r_mcangle_it	2.688
r_mcbond_it	2.357
r_mcbond_other	2.243

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	35.407
r_dihedral_angle_2_deg	33.682
r_dihedral_angle_4_deg	19.021
r_dihedral_angle_3_deg	11.724
r_sphericity_bonded	10.625
r_dihedral_angle_1_deg	5.948
r_rigid_bond_restr	5.935
r_mcangle_it	2.688
r_mcbond_it	2.357
r_mcbond_other	2.243
r_angle_refined_deg	2.02
r_angle_other_deg	0.991
r_chiral_restr	0.141
r_bond_refined_d	0.023
r_gen_planes_refined	0.014
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2436
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
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.