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Structure of Chlorella virus DNA ligase-product DNA complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
experimental model
Other
Structure of Chlorella virus DNA ligase bound to nicked DNA
Crystallization
Crystalization Experiments
ID
Method
pH
Temperature
Details
1
VAPOR DIFFUSION, SITTING DROP
6.5
295
A mixture of ChVLig (230 microM), nicked duplex DNA (220 microM) and 2 mM EDTA was added to an equal volume of a well solution containing 100 mM Bis-Tris-HCl (pH 6.5), 30 mM ammonium acetate, 22% PEG-4000. Crystals were grown at 22 C by the sitting-drop vapor diffusion method. Crystals appeared after 3 days. Crystals of ChVLig in complex with nicked DNA were transferred to a solution containing 100 mM Bis-Tris-HCl (pH 6.5), 110 mM ammonium acetate, 22.5% PEG-4000, 5 mM MnCl2 for 5 min, then placed into a solution containing the same components plus 15% glycerol prior to flash-freezing the crystals in liquid nitrogen., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficient
Solvent content
2.53
51.45
Crystal Data
Unit Cell
Length ( Å )
Angle ( ˚ )
a = 66.475
α = 70.32
b = 92.895
β = 78.45
c = 89.633
γ = 89.87
Symmetry
Space Group
P 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
MAR CCD 165 mm
Double crystal monochromator. Si(111) or Si(220) options. Sagitall focusing. Cylindrically bent ULE mirror with Pt and Rh coating.
2006-05-05
M
SINGLE WAVELENGTH
Radiation Source
ID #
Source
Type
Wavelength List
Synchrotron Site
Beamline
1
SYNCHROTRON
NSLS BEAMLINE X9A
0.9795
NSLS
X9A
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
3
50
95.8
0.078
7.3
1.9
41596
39849
-1
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)
3
3.11
87.7
0.455
1.4
1.7
3651
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
MOLECULAR REPLACEMENT
THROUGHOUT
Structure of Chlorella virus DNA ligase bound to nicked DNA