Experiment: 8IDQ

Crystal structure of reducing-end xylose-releasing exoxylanase in GH30 from Talaromyces cellulolyticus with xylose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6IUJ	homologous protein

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	22% PEG 6000, 0.1 M Tris-HCl, 0.2 M lithium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.249	α = 90
b = 120.159	β = 90
c = 122.886	γ = 90

Symmetry
Space Group	P 21 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	PIXEL	DECTRIS EIGER X 16M		2019-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

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	1.7	45.94	99.2	0.107	0.977	9	4.9		222295			13.71

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76			0.395	0.799	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.7	45.35	1.34	222165	11109	99.13	0.2007	0.199	0.1993	0.2332	0.2331	0

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	6.762
f_angle_d	0.896
f_chiral_restr	0.054
f_bond_d	0.007
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13926
Nucleic Acid Atoms
Solvent Atoms	1625
Heterogen Atoms	1066

Software

Software
Software Name	Purpose
XDS	data scaling
XDS	data reduction
MOLREP	phasing
PHENIX	refinement