Experiment: 8JW3

The crystal structure of the viral terpene synthase from Orpheovirus IHUMI-LCC2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Se substituted OILTS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	0.1 M Citric acid buffer pH 4.5, 1.3 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.442	α = 90
b = 46.763	β = 116.341
c = 69.21	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	95	PIXEL	DECTRIS EIGER X 16M		2022-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	1.45	42.48	99.8	0.023	18.7	6.7		57694			17.06

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.47			0.366	2	6.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	Se substituted OILTS	1.45	42.48	1.34	57678	2912	99.73	0.1776	0.1768	0.1762	0.1929	0.1919	21.84

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	4.509
f_angle_d	0.8381
f_chiral_restr	0.0716
f_plane_restr	0.0089
f_bond_d	0.0055

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2229
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	15

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
Coot	model building
MOLREP	phasing