6UAW

Crystal structure of a GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava (PvGH128_II) in complex with laminaritriose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	bis-tris 0.1 M ammonium sulfate 2 M

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.432	α = 90
b = 33.871	β = 113.11
c = 84.563	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		2018-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.239860	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	1.5	27.18	97.6	0.999	15.36	6.39		36122

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	1.5	1.59			0.838	2.53

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	6UAV	1.5	27.18	34315	1807	97.75	0.1581	0.1562	0.1922	RANDOM	18.233

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]
0.57		-0.55	-0.13		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.042
r_dihedral_angle_4_deg	27.257
r_dihedral_angle_3_deg	12.933
r_dihedral_angle_1_deg	6.819
r_angle_refined_deg	1.953
r_angle_other_deg	1.59
r_chiral_restr	0.108
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.042
r_dihedral_angle_4_deg	27.257
r_dihedral_angle_3_deg	12.933
r_dihedral_angle_1_deg	6.819
r_angle_refined_deg	1.953
r_angle_other_deg	1.59
r_chiral_restr	0.108
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2096
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms	54

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 U.S. National Science Foundation (DBI-2321666), 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.