6UB7

Crystal structure of a GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans (CnGH128_V)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	sodium/potassium phosphate 2.4 M 20% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.896	α = 90
b = 60.066	β = 90
c = 96.085	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 PILATUS 2M		2017-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.458	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	1.8	48.02	98	0.999	13.47	4.56		31515

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	1.8	1.91			0.691

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	28.28	30032	1593	98.17	0.1865	0.1849	0.2176	RANDOM	32.528

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]
-0.03					0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.279
r_dihedral_angle_4_deg	20.112
r_dihedral_angle_3_deg	12.311
r_dihedral_angle_1_deg	7.627
r_mcangle_it	3.169
r_angle_other_deg	2.398
r_mcbond_it	2.134
r_mcbond_other	2.121
r_angle_refined_deg	1.869
r_chiral_restr	0.099

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.279
r_dihedral_angle_4_deg	20.112
r_dihedral_angle_3_deg	12.311
r_dihedral_angle_1_deg	7.627
r_mcangle_it	3.169
r_angle_other_deg	2.398
r_mcbond_it	2.134
r_mcbond_other	2.121
r_angle_refined_deg	1.869
r_chiral_restr	0.099
r_bond_other_d	0.036
r_gen_planes_other	0.022
r_bond_refined_d	0.015
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2068
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	1

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.