8X37

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VPC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	PEG3350, DL-Malic acid

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.26	α = 90
b = 50.27	β = 91.327
c = 120.25	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	80	PIXEL	DECTRIS EIGER X 9M		2021-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1.0	SPring-8	BL32XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.98	50	100	0.124	0.993	8.52	6.6		41220

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.98	2.08	100		2.65	0.75	1.05	6.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	7VPC	1.98	49.165	41220	2061	99.944	0.224	0.2213	0.2744	64.711

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]
-2.42		0.624	7.077		-4.681

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.413
r_dihedral_angle_6_deg	15.29
r_lrange_other	11.086
r_lrange_it	11.084
r_scangle_it	9.083
r_scangle_other	9.082
r_mcangle_it	6.969
r_mcangle_other	6.969
r_dihedral_angle_2_deg	6.061
r_dihedral_angle_1_deg	6.016
r_scbond_it	5.953
r_scbond_other	5.952
r_mcbond_it	4.948
r_mcbond_other	4.947
r_angle_refined_deg	1.471
r_angle_other_deg	0.745
r_symmetry_nbd_refined	0.43
r_nbd_other	0.271
r_nbd_refined	0.228
r_symmetry_nbd_other	0.216
r_xyhbond_nbd_refined	0.192
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.141
r_ncsr_local_group_1	0.137
r_symmetry_xyhbond_nbd_other	0.097
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.068
r_metal_ion_refined	0.038
r_gen_planes_other	0.007
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3818
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
DIALS	data reduction
XDS	data scaling
PHASER	phasing