A PDB coordinate file

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A PDB coordinate file
CRISTALLOGRAFIA
A RAGGI X
Perche’ i raggi X?
• Per vedere un oggetto le sue dimensioni
devono essere almeno la meta’ della lunghezza
d’onda della luce usata per rivelarlo.
• The wavelength of visible light is far from
small enough to see an atom, it is far to big.
X-Rays have short enough wavelengths to
“see” the atoms and the molecular structure
of molecules.
Crystallization*
Crystallization
Protein Crystal
The Setup:
• X-ray Source: x-ray tubes, rotating anode tubes, or particle storage rings
• Gonoimeter
• Detectors: X-ray films, CCD cameras, or Multiwire detectors.
How Does X-Ray Crystallography Work ?
– Image of diffraction
From diffraction to electron
density map
Fourier Transform
To get from the diffraction pattern to the electron density, you have to
use a Fourier Transform.
Resolution
• Resolution: another measure of
how good your model is.
• Resolution gives the size of the
smallest molecule you can see
or resolve.
• Dependent on the amount of
data ultimately phased and used
in structure determination.
The Final Result
ORIGX2
ORIGX3
SCALE1
SCALE2
SCALE3
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
1
2
3
4
5
6
7
8
9
10
11
0.000000
0.000000
0.011173
0.000000
0.000000
N
SER
CA SER
C
SER
O
SER
CB SER
OG SER
N
ASP
CA ASP
C
ASP
O
ASP
CB ASP
1.000000
0.000000
0.000000
0.019585
0.000000
A
1
A
1
A
1
A
1
A
1
A
1
A
2
A
2
A
2
A
2
A
2
0.000000
1.000000
0.004858
0.000000
0.018039
21.389 25.406
21.628 26.691
20.937 26.944
21.072 28.079
21.117 27.770
22.276 27.925
20.173 26.028
19.395 26.125
20.264 26.214
19.760 26.575
18.439 24.914
0.00000
0.00000
0.00000
0.00000
0.00000
-4.628
-3.983
-2.679
-2.093
-5.002
-5.861
-2.163
-0.949
0.297
1.371
-0.856
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
A PDB coordinate file
23.22
24.42
24.21
24.97
28.27
32.61
21.39
21.57
20.89
21.49
22.14
2TRX
2TRX
2TRX
2TRX
2TRX
2TRX
2TRX
2TRX
2TRX
2TRX
2TRX
2TRX
2TRX
2TRX
2TRX
2TRX
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
The PDB
http://www.rcsb.org/pdb/

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