3GB4 | pdb_00003gb4

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		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 anomalous dispersion (SAD) phasing, with assistance from the sulfur anomalous signal in the 2.29 A wavelength data set.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	294	Equal volumes of protein (10-20 mg/mL in 30 mM Tri-HCl,pH 8.0, 0.1 mM EDTA, with trace PMSF) and precipitant solution (15-20%(w/v) PEG 6000 and 0.1 M sodium citrate pH 6.0) were used to make the sitting drop. The data collection crystal was transferred to a cryo-amenable soak solution containing 24% PEG 6000, 24% glycerol, 0.1M HEPES-pH 7, 10 mM CoCl2, and 1.25 mM dicamba for 24 hours prior to being plunge-cooled in liquid nitrogen for data collection, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.55	α = 90
b = 81.55	β = 90
c = 161.29	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		2006-11-11	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	2.05	50	99.6	0.068	23.1	4.1	74823

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)
	2.05	2.12	99.9		0.485	1.66	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	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 anomalous dispersion (SAD) phasing, with assistance from the sulfur anomalous signal in the 2.29 A wavelength data set.	2.05	20	1	2	75230	61905	6177	82.3	0.243	0.225	0.221	0.2	0.262	0.23	random	45.466

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]
-0.026	-0.126		-0.026		0.052

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.937
c_mcangle_it	2.231
c_scbond_it	1.99
c_mcbond_it	1.364
c_angle_deg	1.32
c_bond_d	0.006
c_bond_d_na
c_bond_d_prot
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	7926
Nucleic Acid Atoms
Solvent Atoms	521
Heterogen Atoms	45

Software

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