8Z2X

Crystal structure of exo-beta-(1,3)-glucanase from Aspergillus oryzae (AoBgl) as a complex with cellobiose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CZ1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	1.6M sodium citrate tribasic dihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.89	α = 90
b = 80.89	β = 90
c = 113.69	γ = 120

Symmetry
Space Group	P 32 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	IMAGE PLATE	RIGAKU RAXIS IV++		2020-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.73	38	99.9	0.999	19.78	10.31		45479

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	1.73	1.83			0.883

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	1.73	35.03	43205	2274	99.95	0.13774	0.13687	0.15425	RANDOM	15.98

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]
0.2	0.1		0.2		-0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.67
r_dihedral_angle_4_deg	19.286
r_dihedral_angle_3_deg	12.043
r_dihedral_angle_1_deg	6.575
r_long_range_B_refined	4.927
r_long_range_B_other	4.899
r_scangle_other	4.598
r_scbond_it	3.025
r_scbond_other	3.023
r_mcangle_it	1.96
r_mcangle_other	1.96
r_angle_refined_deg	1.894
r_angle_other_deg	1.617
r_mcbond_it	1.413
r_mcbond_other	1.395
r_chiral_restr	0.104
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2983
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	48

Software

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