3STU

Crystal Structure of tomato Methylketone Synthase I complexed with methyl-3-hydroxydodecanoate

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	0.1M PIPES-Na+, 22% (w/v) PEG 8000, 0.3M NaBr, 2mM dithiothreitol, 2 hr soak in 1mM methyl-3-hydroxydodecanoate, pH 6.5, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.197	α = 90
b = 105.716	β = 96.51
c = 59.888	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 325 mm CCD		2005-05-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.93	39.5	97.8	0.063	24.7	3.7	44670	43407		-3	36.59

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.93	1.97	98.7		0.499	0.499		3.5	2875

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7YAS	1.93	39.5	44670	43407	2186	97.17	0.238	0.2163	0.2149	0.2423	RANDOM	29.1645

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]
-0.01			0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.864
r_dihedral_angle_3_deg	12.943
r_dihedral_angle_4_deg	11.222
r_dihedral_angle_1_deg	5.179
r_scangle_it	1.959
r_scbond_it	1.165
r_angle_refined_deg	1.042
r_mcangle_it	0.939
r_mcbond_it	0.495
r_chiral_restr	0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.864
r_dihedral_angle_3_deg	12.943
r_dihedral_angle_4_deg	11.222
r_dihedral_angle_1_deg	5.179
r_scangle_it	1.959
r_scbond_it	1.165
r_angle_refined_deg	1.042
r_mcangle_it	0.939
r_mcbond_it	0.495
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3969
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	28

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	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.