4W8A

Crystal structure of XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library, in the native form

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291	ammonium sulfate, sodium citrate, glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.951	α = 90
b = 120.951	β = 90
c = 59.03	γ = 120

Symmetry
Space Group	P 61

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	0.954	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	1.72	50	96.9	0.044	0.046	45.99	10.6		50907		-3	17.562

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	1.72	1.82	83.9		0.172

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	MIR	THROUGHOUT	1.72	42.28	49509	2651	95.92	0.1075	0.1054	0.1488	RANDOM	11.214

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]
0.26	0.26		0.26		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.296
r_sphericity_free	23.954
r_dihedral_angle_4_deg	20.117
r_dihedral_angle_3_deg	12.735
r_sphericity_bonded	7.927
r_dihedral_angle_1_deg	6.25
r_rigid_bond_restr	4.813
r_mcangle_it	1.925
r_angle_refined_deg	1.849
r_mcbond_it	1.709

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.296
r_sphericity_free	23.954
r_dihedral_angle_4_deg	20.117
r_dihedral_angle_3_deg	12.735
r_sphericity_bonded	7.927
r_dihedral_angle_1_deg	6.25
r_rigid_bond_restr	4.813
r_mcangle_it	1.925
r_angle_refined_deg	1.849
r_mcbond_it	1.709
r_mcbond_other	1.709
r_angle_other_deg	0.943
r_chiral_restr	0.132
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3012
Nucleic Acid Atoms
Solvent Atoms	493
Heterogen Atoms	38

Software

Software
Software Name	Purpose
XDS	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
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.