Experiment: 5C05

Crystal Structure of Gamma-terpinene Synthase from Thymus vulgaris

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ONG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	298	20 mM Tris, 0.2 M Ammonium tartrate dibasic, 20% w/v Polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.73	55.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.2	α = 94.79
b = 79.61	β = 103.31
c = 93.32	γ = 105.56

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2013-09-12	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2013-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418
2	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97731	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.65		95.7	0.103	0.115	9.19			154186		-3	22.93

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.75	89.2		0.651	0.757	1.96

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	2ONG	1.65	29.84	1.98	154063	1990	95.64	0.1639	0.1636	0.1661	0.1863	0.1884	33.2757

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	12.112
f_angle_d	1.08
f_chiral_restr	0.065
f_bond_d	0.011
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8579
Nucleic Acid Atoms
Solvent Atoms	942
Heterogen Atoms	32

Software

Software
Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building