4W86

Crystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library, in complex with glucose and TRIS

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	PEG3350, PEG400, magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.95	α = 90
b = 96.95	β = 90
c = 95.785	γ = 120

Symmetry
Space Group	P 31

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		2014-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.459	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	2.64	50	96.7	0.135	0.141	16.01	10.8		36412		-3	65.739

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.64	2.8	81.5		1.462

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	2.64	48.52	36412	1466	96.75	0.2157	0.2145	0.2363	RANDOM	64.17

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]
0.85	0.85		0.85		-2.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.23
r_dihedral_angle_4_deg	14.353
r_dihedral_angle_3_deg	11.191
r_dihedral_angle_1_deg	4.907
r_mcangle_it	2.37
r_mcbond_it	1.424
r_mcbond_other	1.424
r_angle_refined_deg	0.877
r_angle_other_deg	0.76
r_chiral_restr	0.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.23
r_dihedral_angle_4_deg	14.353
r_dihedral_angle_3_deg	11.191
r_dihedral_angle_1_deg	4.907
r_mcangle_it	2.37
r_mcbond_it	1.424
r_mcbond_other	1.424
r_angle_refined_deg	0.877
r_angle_other_deg	0.76
r_chiral_restr	0.079
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5380
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	42

Software

Software
Software Name	Purpose
XDS	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
XSCALE	data scaling

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.