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Crystal structure of Escherichia coli YdcF, an S-adenosyl-L-methionine utilizing enzyme
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
experimental model
Other
Structure solved by MAD from the data collected in R3 space group, then molecular replacement using that model for the native single wavelength data collected in P21 space group
Crystallization
Crystalization Experiments
ID
Method
pH
Temperature
Details
1
VAPOR DIFFUSION, HANGING DROP
7.5
298
0.1 M Hepes, 1.7 M Ammonium sulfate, 4 % MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficient
Solvent content
2.64
53.35
Crystal Data
Unit Cell
Length ( Å )
Angle ( ˚ )
a = 64.795
α = 90
b = 39.71
β = 96.34
c = 122.645
γ = 90
Symmetry
Space Group
P 1 21 1
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
ADSC QUANTUM 210
Mirrors
2005-07-01
M
SINGLE WAVELENGTH
Radiation Source
ID #
Source
Type
Wavelength List
Synchrotron Site
Beamline
1
SYNCHROTRON
APS BEAMLINE 17-ID
1.0000
APS
17-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
1.8
50
93.1
0.084
10.3
3.8
54189
54189
18
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)
1
1.8
1.88
93.9
0.228
2.8
3.5
Refinement
Statistics
Diffraction ID
Structure Solution Method
Cross Validation method
Starting model
Resolution (High)
Resolution (Low)
Number Reflections (All)
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
MAD, MOLECULAR REPLACEMENT
THROUGHOUT
Structure solved by MAD from the data collected in R3 space group, then molecular replacement using that model for the native single wavelength data collected in P21 space group