6UBA

Crystal structure of a GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae (AnGH128_VI) in complex with laminaritriose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.18 M tri-ammonium citrate, 18% v/v PEG 3350, 0.01 M Cobalt (II) chloride

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.262	α = 90
b = 152.798	β = 90
c = 169.423	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	PIXEL	DECTRIS PILATUS3 2M		2019-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.458570	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	2.4	49.35	99	0.99	6.24	11.9		123227

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	2.4	2.54			0.602	1.15

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	6UB8	2.4	49.35	117052	6161	99.87	0.2377	0.2367	0.2556	RANDOM	35.357

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]
6.36			-4.52		-1.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.172
r_dihedral_angle_4_deg	19.086
r_dihedral_angle_3_deg	15.005
r_dihedral_angle_1_deg	6.832
r_angle_refined_deg	1.276
r_angle_other_deg	1.11
r_chiral_restr	0.051
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.172
r_dihedral_angle_4_deg	19.086
r_dihedral_angle_3_deg	15.005
r_dihedral_angle_1_deg	6.832
r_angle_refined_deg	1.276
r_angle_other_deg	1.11
r_chiral_restr	0.051
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20305
Nucleic Acid Atoms
Solvent Atoms	699
Heterogen Atoms	559

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	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.