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Crystal Structure of Dicamba Monooxygenase with Non-heme Cobalt and DCSA
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 a high-redundancy, 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 Tris-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, 0.1 M HEPES pH 7.0, 10 mM CoCl2, and 1.25 mM DCSA 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
2.63
53.19
Crystal Data
Unit Cell
Length ( Å )
Angle ( ˚ )
a = 81.01
α = 90
b = 81.01
β = 90
c = 161.05
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
99.5
0.069
22.8
4
73721
73352
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
0.451
1.91
4
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 (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 a high-redundancy, 2.29 A wavelength data set.