5HC7

Crystal structure of lavandulyl diphosphate synthase from Lavandula x intermedia in complex with S-thiolo-isopentenyldiphosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1V7U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	Ammonium Sulfate, Glycerol, PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.392	α = 90
b = 141.606	β = 90
c = 78.918	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX-300		2015-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1.0	NSRRC	BL15A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.05	25	98.9	0.056	0.066	0.035	9.8	3.5		19241

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.12	93.4		0.42	0.498	0.265	0.853		3.3	1783

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1V7U	2.05	25	18346	879	98.59	0.1707	0.1685	0.2144	RANDOM	44.861

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]
-2.21			4.31		-2.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.086
r_dihedral_angle_4_deg	23.124
r_dihedral_angle_3_deg	16.593
r_dihedral_angle_1_deg	6.413
r_mcangle_it	4.788
r_mcbond_it	3.569
r_mcbond_other	3.568
r_angle_refined_deg	2.077
r_angle_other_deg	1.003
r_chiral_restr	0.132

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.086
r_dihedral_angle_4_deg	23.124
r_dihedral_angle_3_deg	16.593
r_dihedral_angle_1_deg	6.413
r_mcangle_it	4.788
r_mcbond_it	3.569
r_mcbond_other	3.568
r_angle_refined_deg	2.077
r_angle_other_deg	1.003
r_chiral_restr	0.132
r_bond_refined_d	0.024
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1853
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.