Experiment: 9LF6

Crystal of Glucosidase form Gelsemium sempervirens

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277.15	Purified GsSGD proteins at a concentration of 8 mg/mL and vincosamide were combined with an equal volume of reservoir solution containing 0.13 M lithium sulfate, 0.1 M sodium citrate tribasic dihydrate and 20% PEG1000 at pH of 5.8.The crystal crystallization conditions were optimized under this condition using the Additive Screen kit (Salt: 30% v/v methanol; Classification: organic, volatile; Suggested drop concentration: 3.0%) Diffraction-quality crystals were produced within a time-frame of 14 days.

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 237.43	α = 90
b = 107.84	β = 118.46
c = 220.27	γ = 90

Symmetry
Space Group	C 1 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	277.15	PIXEL	DECTRIS PILATUS3 6M		2024-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97861	SSRF	BL19U1

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	2.95	48.99	95.77	0.961	6.25	4.03		98923			22.04

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	2.95	3.055			0.726

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.95	48.99	1.34	98839	4953	95.8	0.2084	0.2063	0.2066	0.2482	0.247	14.6

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.1665
f_angle_d	1.2184
f_chiral_restr	0.0646
f_bond_d	0.0125
f_plane_restr	0.0081

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	29229
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	105

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing