6UB4

Crystal structure (C2 form) of a GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	ammonium sulfate 1.4 M 10% dioxane MMT 0.1 M

Crystal Properties
Matthews coefficient	Solvent content
3.46	64.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.775	α = 90
b = 46.52	β = 119.5
c = 114.786	γ = 90

Symmetry
Space Group	C 1 2 1

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 PILATUS 2M		2019-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.03316	LNLS	W01B-MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.6	28.9	96.7	0.999	12.36	6.5		92515

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	1.6	1.7			0.75	1.46

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	6UB2	1.6	28.9	87867	4625	96.81	0.1817	0.1802	0.2098	RANDOM	24.877

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]
0.47		-0.29	-2.96		1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.791
r_dihedral_angle_4_deg	23.739
r_dihedral_angle_3_deg	10.944
r_dihedral_angle_1_deg	7.276
r_angle_refined_deg	1.693
r_angle_other_deg	1.557
r_chiral_restr	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.791
r_dihedral_angle_4_deg	23.739
r_dihedral_angle_3_deg	10.944
r_dihedral_angle_1_deg	7.276
r_angle_refined_deg	1.693
r_angle_other_deg	1.557
r_chiral_restr	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3724
Nucleic Acid Atoms
Solvent Atoms	640
Heterogen Atoms	94

Software

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

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.