8KAQ

Glycoside hydrolase family 1 beta-glucosidase (E318G mutant) from Streptomyces griseus (sophorose complex)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4R27

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M Bis-Tris propane (pH 6.5), 0.3 M sodium formate, 18% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.793	α = 90
b = 100.179	β = 102.868
c = 96.048	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS3 S 6M		2022-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1	Photon Factory	BL-5A

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	2.13	46.824	98.7	0.995	10.4	3.4		93387

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	2.13	2.17			0.637

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.13	46.824	93364	4704	98.515	0.185	0.1833	0.2233	28.114

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]
-0.66		0.004	0.218		0.399

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.875
r_dihedral_angle_3_deg	15.307
r_dihedral_angle_2_deg	7.831
r_dihedral_angle_1_deg	6.778
r_lrange_it	5.337
r_lrange_other	5.3
r_scangle_it	4.082
r_scangle_other	4.082
r_mcangle_it	3.178
r_mcangle_other	3.178
r_scbond_it	2.611
r_scbond_other	2.611
r_mcbond_it	2.152
r_mcbond_other	2.151
r_angle_refined_deg	1.372
r_angle_other_deg	0.488
r_nbd_refined	0.232
r_symmetry_nbd_other	0.205
r_nbd_other	0.195
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.152
r_symmetry_nbd_refined	0.145
r_symmetry_xyhbond_nbd_refined	0.136
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.065
r_symmetry_xyhbond_nbd_other	0.033
r_chiral_restr_other	0.007
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12145
Nucleic Acid Atoms
Solvent Atoms	529
Heterogen Atoms	163

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
ARP/wARP	model building
MOLREP	phasing
Aimless	data scaling