3STX

Crystal Structure of tomato Methylketone Synthase I H243A variant complexed with beta-ketoheptanoate

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	7	277	0.1M MOPSO-Na+, 15% (w/v) PEG 8000, 0.3M NaBr, 2mM dithiothreitol, overnight soak in 1mM beta-ketoheptanoate, pH 7.0, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.237	α = 90
b = 94.387	β = 97.59
c = 60.077	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	ADSC QUANTUM 315		2007-08-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0	ALS	8.2.2

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	2.3	19.6	88.8	0.118	11.19	4.1	21097	21096		-3	32.115

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	2.3	19.37	21097	21093	1083		0.235	0.2086	0.2052	0.2728	RANDOM	28.3783

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

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.208
r_dihedral_angle_3_deg	15.441
r_dihedral_angle_4_deg	13.444
r_dihedral_angle_1_deg	5.361
r_scangle_it	1.445
r_angle_refined_deg	1.111
r_scbond_it	0.885
r_mcangle_it	0.865
r_mcbond_it	0.476
r_chiral_restr	0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.208
r_dihedral_angle_3_deg	15.441
r_dihedral_angle_4_deg	13.444
r_dihedral_angle_1_deg	5.361
r_scangle_it	1.445
r_angle_refined_deg	1.111
r_scbond_it	0.885
r_mcangle_it	0.865
r_mcbond_it	0.476
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	3944
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	20

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
XDS	data reduction
XDS	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.