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Structural insights into catalytic and substrate binding mechanisms of the strategic EndA nuclease from Streptococcus pneumoniae
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
experimental model
Other
incomplete manually built model of EndA from a low resolution incompletely refined data set from an MBP-EndA fusion protein
Crystallization
Crystalization Experiments
ID
Method
pH
Temperature
Details
1
VAPOR DIFFUSION, SITTING DROP
7
297
Crystallization solution contained 0.1M Tris pH 7, 17% PEG8000, and 0.2M MgCl2. The crystal was transferred to a hanging drop containing 0.1M Tris pH 7, 75mM MaCl, 0.2M MgCl2, and 20% PEG800, which was then placed over a vapor diffusion chamber containing a sitting drop bridge with 25% glutaraldehyde. The crystal was cross-linked for 8 minutes at room temperature, then transferred to a soaking solution containing 0.1M Tris pH 7, 75mM NaCl, 0.2M MgCl2,20% PEG8000, 11.6mM trimethyl lead acetate, and 9.63mM triethyl lead acetate for 43 hrs at room temperature. The soaked crystal was then transferred to a cryoprotectant (0.1M Tris pH 7, 75mM NaCl, 0.2M MgCl2, 20% PEG8000, 15% ethylene glycol, 11.9mM trimethyl lead acetate, and 13.75mM triethyl lead acetate) in four steps, then flash frozen in liquid nitrogen. , VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties
Matthews coefficient
Solvent content
2.19
43.72
Crystal Data
Unit Cell
Length ( Å )
Angle ( ˚ )
a = 67.963
α = 90
b = 75.931
β = 90
c = 90.784
γ = 90
Symmetry
Space Group
P 21 21 21
Diffraction
Diffraction Experiment
ID #
Crystal ID
Scattering Type
Data Collection Temperature
Detector
Detector Type
Details
Collection Date
Monochromator
Protocol
1
1
x-ray
93
CCD
MARMOSAIC 225 mm CCD
2009-12-10
M
SINGLE WAVELENGTH
Radiation Source
ID #
Source
Type
Wavelength List
Synchrotron Site
Beamline
1
SYNCHROTRON
APS BEAMLINE 22-ID
0.94
APS
22-ID
Data Collection
Overall
ID #
Resolution (High)
Resolution (Low)
Percent Possible (Observed)
R Sym 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
1.75
50
96.8
0.097
26.5
13.6
46402
46402
-3
-3
17.8
Highest Resolution Shell
ID #
Resolution (High)
Resolution (Low)
Percent Possible (All)
Percent Possible (Observed)
R-Sym I (Observed)
Mean I Over Sigma (Observed)
Redundancy
Number Unique Reflections (All)
1.75
1.78
68.7
0.371
3.56
7.2
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-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
incomplete manually built model of EndA from a low resolution incompletely refined data set from an MBP-EndA fusion protein