6UBB | pdb_00006ubb

Crystal structure of a GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae (AnGH128_VI) with laminaribiose at the surface-binding site

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.18 M tri-ammonium citrate, 18% v/v PEG 3,350, 0.01 M Cobalt (II) chloride

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.349	α = 90
b = 152.733	β = 90
c = 169.135	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	2.35	50	99.9	0.98	4.8	6.7		130821

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	2.35	2.49			0.433

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.35	49.3	130808	6541	99.8	0.265	0.27	0.301	0.3	33.87

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]
3.831			-2.842		-0.989

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.255
r_dihedral_angle_4_deg	18.212
r_dihedral_angle_3_deg	15.859
r_dihedral_angle_1_deg	6.534
r_angle_other_deg	2.474
r_angle_refined_deg	1.193
r_mcangle_it	0.882
r_mcangle_other	0.882
r_scangle_it	0.556
r_scangle_other	0.556
r_mcbond_it	0.47
r_mcbond_other	0.47
r_scbond_it	0.291
r_scbond_other	0.291
r_nbd_refined	0.165
r_nbd_other	0.162
r_nbtor_refined	0.155
r_xyhbond_nbd_refined	0.098
r_chiral_restr	0.042
r_bond_other_d	0.035
r_gen_planes_other	0.003
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20310
Nucleic Acid Atoms
Solvent Atoms	477
Heterogen Atoms	230

Software

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