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Crystal Structure of Dicamba Monooxygenase with Non-heme Cobalt 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 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.