8X35

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form A)

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	DL-malic acid, PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.31	α = 90
b = 49.23	β = 91.067
c = 121.39	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)	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	1.92	50	100	0.994	9.7	11.7		44740

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	1.92	2.04	100		3.1	0.771	1.07	12

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	1.92	49.146	44740	2237	99.989	0.221	0.219	0.2566	49.366

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]
-2.084		0.056	5.321		-3.236

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.347
r_dihedral_angle_6_deg	17.857
r_lrange_it	6.731
r_lrange_other	6.729
r_scangle_it	5.744
r_scangle_other	5.743
r_dihedral_angle_1_deg	5.725
r_dihedral_angle_2_deg	5.549
r_scbond_it	4.086
r_scbond_other	4.085
r_mcangle_other	3.892
r_mcangle_it	3.89
r_mcbond_it	2.846
r_mcbond_other	2.846
r_angle_refined_deg	1.566
r_angle_other_deg	0.735
r_nbd_other	0.267
r_symmetry_nbd_refined	0.232
r_nbd_refined	0.22
r_symmetry_nbd_other	0.22
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_other	0.134
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.069
r_metal_ion_refined	0.043
r_symmetry_xyhbond_nbd_refined	0.035
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_gen_planes_other	0.005
r_bond_other_d	0.002
r_dihedral_angle_other_2_deg	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3778
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	59

Software

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