7AX7

Crystal structure of the Xyl-CE4 domain of a multidomain xylanase from the hindgut metagenome of Trinervitermes trinervoides

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C71

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292.2	10 mg/mL in 20 mM Tris-HCl pH 7.5, 10 mM NaCl, 8 % (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.13	α = 90
b = 59.7	β = 90
c = 86.1	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	RIGAKU SATURN 944		2017-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	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	1.93	23.07	99	0.019	0.999	2.74	2		13512			13.713555817

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.12	96.9		0.991

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2C71	2.05000181627	19.5413775456	1.4376150803	13512	683	99.8817267889	0.176291932968	0.172865563929	0.24277939068	14.1404325504

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.4408772302
f_angle_d	0.707693815628
f_chiral_restr	0.0485426672537
f_bond_d	0.00635143631305
f_plane_restr	0.00427123583596

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1610
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	5

Software

Software
Software Name	Purpose
HKL-3000	data collection
d*TREK	data reduction
d*TREK	data scaling
d*TREK	data processing
d*TREK	data scaling
PHASER	phasing
PHASER	refinement

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.