9U98 | pdb_00009u98

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	8KAP

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% PEG 3350

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 6M		2022-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.13	46.818	93364	4704	98.515	0.183	0.1808	0.1899	0.2278	0.2327	28.303

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]
-0.007		0.002	0.002		0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.723
r_dihedral_angle_3_deg	14.492
r_dihedral_angle_2_deg	9.658
r_dihedral_angle_1_deg	6.883
r_lrange_it	5.929
r_lrange_other	5.897
r_scangle_it	4.751
r_scangle_other	4.751
r_mcangle_it	3.702
r_mcangle_other	3.702
r_scbond_it	3.182
r_scbond_other	3.181
r_mcbond_it	2.622
r_mcbond_other	2.621
r_angle_refined_deg	1.666
r_angle_other_deg	0.926
r_nbd_refined	0.238
r_nbd_other	0.215
r_symmetry_nbd_other	0.214
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.151
r_symmetry_nbd_refined	0.133
r_symmetry_xyhbond_nbd_refined	0.111
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.036
r_gen_planes_other	0.01
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_chiral_restr_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12145
Nucleic Acid Atoms
Solvent Atoms	530
Heterogen Atoms	162

Software

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