Experiment: 9LFR

Crystal of Glucosidase form Ophiorrhiza pumila

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZJ6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	291.15	Purified OpBGlu1 proteins at a concentration of 6 mg/mL was combined with an equal volume of reservoir solution containing 0.1 M sodium acetate at pH of 4.6 and 2.0 ammonium sulfate. Consistent with the conditions under which loganetin was added, the reservoir solution consisted of 0.1 M sodium acetate trihydrate at pH 4.5 and 2.0 M ammonium sulfate. The sessile drop plate was covered with an adhesive tape and incubated in a cabinet maintained at a temperature of 291.15 K. Diffraction-quality crystals were produced within a time-frame of 10 to 15 days.

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.99	α = 90
b = 136.99	β = 90
c = 164.75	γ = 90

Symmetry
Space Group	I 4 2 2

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 PILATUS 6M		2024-06-21	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	1.78	82.38	99.82	1	22.92	1.999		74660			19.29

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	1.78	1.844			0.617

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	1.78	82.38	1.34	74644	2000	99.82	0.1939	0.1932	0.1932	0.2185	0.2177	21.66

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	6.447
f_angle_d	0.8965
f_chiral_restr	0.0558
f_plane_restr	0.0089
f_bond_d	0.0075

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3780
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	10

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPX	data reduction
Aimless	data scaling
PHENIX	phasing