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Crystal Structure of Dicamba Monooxygenase with Non-heme Iron and Dicamba
X-RAY DIFFRACTION
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 wavelength anomalous dispersion (SAD) phasing, with assistance from the sulfur anomalous signal in a high-redundancy, 2.29 A wavelength data set.
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 (Depositor)
R-Work (DCC)
R-Free (Depositor)
R-Free (DCC)
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.