3GTS

Crystal Structure of Dicamba Monooxygenase with Non-heme Iron and Dicamba

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	294	The purified protein was concentrated to 10-20 mg/ml and buffer exchanged into 25 mM Tris-HCl, pH 8.0, 30-50 mM NaCl, 25 mM sodium citrate. DMO crystals were grown using the vapor diffusion by sitting drop method, with a reservoir solution of 8-11% PEG 6000, 100 mM sodium acetate buffer-pH 5.5, 1 M LiCl, and 4ul droplets of varying protein-to-precipitant ratios. To prepare a DMO-non-heme iron-dicamba crystal, some crystals were transferred to a cryo-amenable storage solution that contained 25 mM dicamba (12.3 % PEG6000, 95 mM sodium acetate pH 5.5, 21% glycerol, 1mM NaN3, and 25 mM dicamba) for 5-6 hours prior to plunge-cooling for cryo-storage and low temperature data collection. VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.8	α = 90
b = 80.8	β = 90
c = 159.6	γ = 120

Symmetry
Space Group	P 32

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 300 mm CCD		2005-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

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	2.2	36.04	99.7	0.056	27.6	4	59051	58874

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.28	100		0.419		4

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-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	MR was performed using a preliminary DMO structure. This early DMO structure was obtained largely using a high-redundancy, 1.5418 A wavelength data set for Fe single wavelength anomalous dispersion (SAD) phasing, with assistance from the sulfur anomalous signal in a high-redundancy, 2.29 A wavelength data set.	2.2	20	50201	5057	84.9	0.23	0.266	random	47.933

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]
-0.098	-0.04		-0.098		0.196

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.618
c_mcangle_it	2.146
c_scbond_it	1.81
c_angle_deg	1.32
c_mcbond_it	1.302
c_bond_d	0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7809
Nucleic Acid Atoms
Solvent Atoms	483
Heterogen Atoms	40

Software

Software
Software Name	Purpose
SERGUI	data collection
PHASER	phasing
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling