4PMV

Crystal structure of a novel reducing-end xylose-releasing exo-oligoxylanase (XynA) belonging to GH10 family (space group P43212)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PMU

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.819	α = 90
b = 78.819	β = 90
c = 303.969	γ = 90

Symmetry
Space Group	P 43 21 2

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	3	50	97.4	0.16	5.3	10.4		19710

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	3	3.05	99		0.704		11.6	978

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	4PMU	3.001	48.14	19574	996	97.05	0.2269	0.2255	0.2531	RANDOM	59.228

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]
-0.76			-0.76		1.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.543
r_dihedral_angle_4_deg	17.368
r_dihedral_angle_3_deg	15.809
r_dihedral_angle_1_deg	4.904
r_mcangle_it	1.532
r_scbond_it	0.929
r_angle_refined_deg	0.922
r_mcbond_it	0.898
r_chiral_restr	0.066
r_bond_refined_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.543
r_dihedral_angle_4_deg	17.368
r_dihedral_angle_3_deg	15.809
r_dihedral_angle_1_deg	4.904
r_mcangle_it	1.532
r_scbond_it	0.929
r_angle_refined_deg	0.922
r_mcbond_it	0.898
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	5628
Nucleic Acid Atoms
Solvent Atoms	23
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 R01GM157729.