Some Atomic Constants Data Table

Xiangyun Qiu

Date: July 30, 2005

Supported atomic (group) types for solution

scattering calculations
The tabulated values come into existence for various reasons.
Z & Charge
Scattering contrast is proportional to the number of electrons, not protons. This
necessitates the use of exact number of electrons for ions.
Hydrated Radius
They are used for computing the excluded volume of the macromolecule, as well as the
surface mapping, and hydration shell extraction. For neutral atoms, the hydration radius
is simply taken as the van derr waals radius, which is the distance between non-bound
atoms upon contact.

For organic atoms (groups), data sources are used in the order of preference: CRYSOL
paper by Svergun et al. [1] (only for some organic atomic groups though, which were
claimed to be measured values by Fraser et al. [2]), the improved cube method (ICM)
paper by Palvov and Fedorov [3] (only for some organic atom group, the values from
Bondi's compilation, compared to used in Lee and Richard's original cube method paper).
Note that the ``H+'' ionic radius is the ``H3O+'' radius.

For ions, the hydrated ionic radii are taken from page 73 of book ionic hydration in
chemistry and biophysics by B.E. Conway. The number appears somewhat rather large to
me. For example, a web resource (http://www.bbc.co.uk/dna/h2g2/A1002709) gives the
group I ionic hydration radii as Li+(3.40), Na+(2.76), K+(2.32), Rb+(2.28), Cs+(2.28).
All are substantially smaller than Conway's numbers.

Excluded volume
The scattering contrast in solution needs to be corrected for excluded volume effect. For
organic atoms, the excluded volume is simply the expelled volume, and values are taken
from CYSOL paper (actually the web source is used) by Svergun [1]. For charged ions,
the situation is more complicated due to the denser hydration shells. The solvent
hydration shells is divided into fours regions: the primary hydration shell, the secondary
 hydration shell, the disordered layer, and the bulk solvent. In fact, the hydration volume
is used for excluded volume, and is taken from page 59 of book ions in solution by John
Burgess. The concept of hydration volume is the total solution volume change caused by
addition of a singe ion.
Effective Z
This is the real scattering contrast of each atom/ion in solution, obtained by

. Apparently, this is a crude approximation, which loses

accuracy at high . However, as we are mostly interested in low region, the

introduced uncertainty is expected to be small.

Table 1: Atomic (group) types supported for solution small angle scattering calculations
* Z charge hydrated radius (A) excluded volume (A3) eff. Z
C 6 0 1.74 16.4400 0.50
CH 7 0 2.00 21.5900 -0.22
CH2 8 0 2.00 26.7400 -0.95
CH3 9 0 2.00 31.8900 -1.67
N 7 0 0.84 2.4900 6.17
NH 8 0 1.65 7.6400 5.44
NH2 9 0 1.70 12.7900 4.72
NH3 10 0 2.00 17.9400 4.00
O 8 0 1.50 9.1300 4.95
OH 9 0 1.60 14.2800 4.22
S 16 0 1.68 19.8600 9.35
SH 17 0 1.81 25.1000 8.60
P 15 0 1.11 5.7300 13.08
FE 23 3 0.00 -94.9829 54.78
CU 27 2 0.00 0.0000 27.00
CA 18 2 4.12 -34.3732 29.50
MG 10 2 4.28 -39.6878 23.28
MN 23 2 0.00 0.0000 23.00
ZN 28 2 4.30 0.0000 28.00
 H 0 1 2.80 -2.4742 0.83
NA 10 1 3.58 -4.9816 11.67
K 18 1 3.31 12.1219 13.94
RB 36 1 3.29 20.4246 29.17
CS 54 1 3.29 32.7126 43.05
SR 36 2 4.12 -35.2035 47.78
CO 72 3 0.00 118.7452 32.27
Cl 18 -1 3.32 27.0834 8.94
BR 36 -1 3.30 38.5420 23.10

Hydrogen atoms in PDB entries

Either for simplicity or the uncertainty in experimental determinations, Hydrogen atoms are
usually not included in the PDB files. Thus, the need comes to add them for scattering contrast
and excluded volume calculations. The table is extracted from CRYSOL website
http://www.embl-hamburg.de/ExternalInfo/Research/Sax/manual_crysol.html.

Table 2: Nucleic acids atomic (group) types corresponding to the data base entries above.
* ADE GUA CYT URI THY GTP
OXT 9 9 9 9 9 9
P 13 13 13 13 13 0
O1P 9 9 9 9 9 9
O2P 10 9 9 9 9 9
C5* 3 3 3 3 3 3
C4* 2 2 2 2 2 2
C3* 2 2 2 2 2 2
C2* 2 2 2 2 2 2
C1* 2 2 2 2 2 2
O5* 9 9 9 9 9 9
O4* 9 9 9 9 9 9
 O3* 9 9 9 9 9 9
O2* 10 9 9 9 0 9
N9 5 5 0 0 0 5
N7 5 5 0 0 0 5
N6 7 0 0 0 0 0
N4 0 0 7 0 0 0
N3 5 5 5 6 5 5
N2 0 7 0 0 0 7
N1 5 6 5 5 5 6
N23 0 0 0 0 0 5
C8 2 2 0 0 0 2
C6 1 1 2 2 2 1
C5 1 1 2 2 1 1
C4 1 1 1 1 1 1
C2 2 1 1 1 1 1
O6 0 9 0 0 0 9
O4 0 0 0 9 9 0
O2 0 0 9 9 9 9
P3 0 0 0 0 0 13
P2 0 0 0 0 0 13
P1 0 0 0 0 0 13
C5M 0 0 0 0 4 0

Table 3: Atomic constant table of some physical properties.

Inco
Ato CoherentSc here
Atomi Covale Boilin Melti Densi Atom Absorpti
mic atteringLen ntX-
* Z cRadi ntRadi gPoin ngPoi ty[g/c icVol on@1.8A
Mas gth[1E- secti
us[A] us[A] t[K] nt[K] cm] ume [barn]
s 12cm] on[b
arn]
H 1 0.79 0.32 1.00 20.26 14.02 0.089 14.40 -0.37400 79.9 0.3326
 7940 80 50 9 0 000
0
4.00
H 4.215 0.950 0.178 0.00
2 0.49 0.93 2602 0.000 0.32600 0.0075
E 0 0 7 00
0
6.94
L 1615. 453.7 0.530 13.10 0.91
3 2.05 1.23 1000 -0.19000 70.5000
I 0000 000 0 0 00
0
9.01
B 2745. 1560. 1.850 0.00
4 1.40 0.90 2182 5.000 0.77900 0.0076
E 0000 0000 0 50
0
10.8
4275. 2300. 2.340 1.70
B 5 1.17 0.82 1100 4.600 0.53000 767.0000
0000 0000 0 00
00
12.0
4470. 4100. 2.620 0.00
C 6 0.91 0.77 1100 4.580 0.66480 0.0035
0000 0000 0 10
00
14.0
77.35 63.14 1.251 17.30 0.49
N 7 0.75 0.75 0674 0.93600 1.9000
00 00 0 0 00
00
15.9
90.18 50.35 1.429 14.00 0.00
O 8 0.65 0.73 9940 0.58050 0.0002
00 00 0 0 00
00
18.9
84.95 53.48 1.696 17.10 0.00
F 9 0.57 0.72 9840 0.56540 0.0096
00 00 0 0 08
32
20.1
N 1 27.09 24.55 0.901 16.70 0.00
0.51 0.71 7970 0.45470 0.0390
E 0 60 30 0 0 80
00
22.9
N 1 1156. 371.0 0.970 23.70 1.62
2.23 1.54 8976 0.36300 0.5300
A 1 0000 000 0 0 00
80
24.3
M1 1363. 922.0 1.740 13.97 0.07
1.72 1.36 0500 0.53750 0.0630
G 2 0000 000 0 0 70
00
26.9
A 1 2793. 933.2 2.700 10.00 0.00
1.82 1.18 8153 0.34490 0.2310
L 3 0000 500 0 0 85
90
 28.0
S 1 3540. 1685. 2.330 12.10 0.01
1.46 1.11 8550 0.41490 0.1710
I 4 0000 0000 0 0 50
00
30.9
1 550.0 317.3 1.820 17.00 0.00
P 1.23 1.06 7362 0.51300 0.1720
5 000 000 0 0 60
00
32.0
1 717.7 388.3 2.070 15.50 0.00
S 1.09 1.02 6600 0.28470 0.5300
6 500 600 0 0 70
00
35.4
C 1 239.1 172.1 3.170 22.70 5.20
0.97 0.99 5270 0.95792 33.5000
L 7 000 600 0 0 00
00
39.9
A 1 87.30 83.81 1.784 28.50 0.22
0.88 0.98 4800 0.19090 0.6750
R 8 00 00 0 0 00
00
39.0
1 1032. 336.3 0.860 45.46 0.25
K 2.77 2.03 9830 0.37100 2.1000
9 0000 500 0 0 00
00
40.0
C 2 1757. 1112. 1.550 29.90 0.03
2.23 1.91 7800 0.49000 0.4300
A 0 0000 0000 0 0 00
00
44.9
S 2 3104. 1812. 3.000 15.00 4.50
2.09 1.62 5591 1.22900 27.2000
C 1 0000 0000 0 0 00
00
47.8
T 2 3562. 1943. 4.500 10.64 2.67
2.00 1.45 8000 -0.33000 6.0900
I 2 0000 0000 0 0 00
00
50.9
2 3682. 2175. 5.800 5.18
V 1.92 1.34 4150 8.780 -0.03820 5.0800
3 0000 0000 0 70
00
51.9
C 2 2945. 2130. 7.190 1.83
1.85 1.18 9610 7.230 0.36350 3.0700
R 4 0000 0000 0 00
00
54.9
M2 2335. 1517. 7.430 0.40
1.79 1.17 3085 1.390 -0.37300 13.3000
N 5 0000 0000 0 00
00
55.8
F 2 3135. 1809. 7.860 0.39
1.72 1.17 4700 7.100 0.95400 2.5600
E 6 0000 0000 0 00
00
 58.9
C 2 3201. 1768. 8.900 4.80
1.67 1.16 3320 6.700 0.25000 37.1800
O 7 0000 0000 0 00
00
58.6
N 2 3187. 1726. 8.900 5.20
1.62 1.15 9000 6.590 1.03000 4.4900
I 8 0000 0000 0 00
00
63.5
C 2 2836. 1357. 8.960 0.52
1.57 1.17 4600 7.100 0.77180 3.7800
U 9 0000 6000 0 00
00
65.3
Z 3 1180. 692.7 7.140 0.07
1.53 1.25 9000 9.200 0.56800 1.1100
N 0 0000 300 0 70
00
69.7
G 3 2478. 302.9 5.910 11.80 0.00
1.81 1.26 2300 0.72880 2.9000
A 1 0000 000 0 0 00
00
72.6
G 3 3107. 1210. 5.320 13.60 0.17
1.52 1.22 1000 0.81929 2.3000
E 2 0000 4000 0 0 00
00
74.9
A 3 876.0 1081. 5.720 13.10 0.06
1.33 1.20 2159 0.65800 4.5000
S 3 000 0000 0 0 00
00
78.9
S 3 958.0 494.0 4.800 16.45 0.33
1.22 1.16 6000 0.79700 11.7000
E 4 000 000 0 0 00
00
79.9
B 3 332.2 265.9 3.120 23.50 0.10
1.12 1.14 0400 0.67900 6.9000
R 5 500 000 0 0 00
00
83.8
K 3 119.8 115.7 3.740 38.90 0.03
1.03 1.12 0000 0.78000 25.0000
R 6 000 800 0 0 00
00
85.4
R 3 961.0 312.6 1.530 55.90 0.30
2.98 2.16 6780 0.70800 0.3800
B 7 000 400 0 0 00
00
87.6
S 3 1650. 1041. 2.600 33.70 0.04
2.45 1.91 2000 0.70200 1.2800
R 8 0000 0000 0 0 00
00
88.9
3 3611. 1799. 4.500 19.80 0.15
Y 2.27 1.62 0585 0.77500 1.2800
9 0000 0000 0 0 00
00
 91.2
Z 4 4682. 2125. 6.490 14.10 0.16
2.16 1.45 2400 0.71600 0.1850
R 0 0000 0000 0 0 00
00
92.9
N 4 5017. 2740. 8.550 10.87 0.00
2.09 1.34 0638 0.70540 1.1500
B 1 0000 0000 0 0 24
00
95.9
M4 4912. 2890. 10.20 0.28
2.01 1.30 4000 9.400 0.69500 2.5500
O 2 0000 0000 00 00
00
98.9
T 4 4538. 2473. 11.50 0.00
1.95 1.27 1000 8.500 0.68000 20.0000
C 3 0000 0000 00 00
00
101.
R 4 4423. 2523. 12.20 0.07
1.89 1.25 0700 8.300 0.72100 2.5600
U 4 0000 0000 00 00
000
102.
R 4 3970. 2236. 12.40 0.00
1.83 1.25 9055 8.300 0.58800 145.0000
H 5 0000 0000 00 00
000
106.
P 4 3237. 1825. 12.00 0.09
1.79 1.28 4200 8.900 0.59100 6.9000
D 6 0000 0000 00 30
000
107.
A 4 2436. 1234. 10.50 10.30 0.58
1.75 1.34 8682 0.59220 63.3000
G 7 0000 0000 00 0 00
000
112.
C 4 1040. 594.1 8.650 13.10 2.40 2520.000
1.71 1.48 4110 0.51000
D 8 0000 800 0 0 00 0
000
114.
I 4 2346. 429.7 7.310 15.70 0.54
2.00 1.44 8200 0.40650 193.8000
N 9 0000 600 0 0 00
000
118.
S 5 2876. 505.0 7.300 16.30 0.02
1.72 1.41 7100 0.62280 0.6260
N 0 0000 600 0 0 20
000
121.
S 5 1860. 904.0 6.680 18.23 0.30
1.53 1.40 7500 0.56410 5.1000
B 1 0000 000 0 0 00
000
127.
T 5 1261. 722.6 6.240 20.50 0.02
1.42 1.36 6000 0.54300 4.7000
E 2 0000 500 0 0 00
000
 126.
5 458.4 386.7 4.920 25.74 0.00
I 1.32 1.33 9044 0.52800 6.2000
3 000 000 0 0 00
700
131.
X 5 165.0 161.3 5.890 37.30 0.00
1.24 1.31 2900 0.48500 23.9000
I 4 300 600 0 0 00
000
132.
C 5 944.0 301.5 1.870 71.07 0.21
3.34 2.35 9054 0.54200 29.0000
S 5 000 500 0 0 00
300
137.
B 5 2171. 1002. 3.500 39.24 0.01
2.78 1.98 3270 0.52500 1.2000
A 6 0000 0000 0 0 00
000
138.
L 5 3730. 1193. 6.700 20.73 1.13
2.74 1.69 9055 0.82400 8.9700
A 7 0000 0000 0 0 00
000
140.
C 5 3699. 1071. 6.780 20.67 0.00
2.70 1.65 1150 0.48400 0.6300
E 8 0000 0000 0 0 00
000
140.
P 5 3785. 1204. 6.770 20.80 0.01
2.67 1.65 9076 0.44500 11.5000
R 9 0000 0000 0 0 60
500
144.
N 6 3341. 1289. 7.000 20.60 11.0
2.64 1.64 2400 0.76900 50.5000
D 0 0000 0000 0 0 000
000
145.
P 6 3785. 1204. 6.475 22.39 1.30
2.62 1.63 0000 1.26000 168.4000
M1 0000 0000 0 0 00
000
150.
S 6 2064. 1345. 7.540 19.95 50.0 5670.000
2.59 1.62 3600 0.42000
M2 0000 0000 0 0 000 0
000
151.
E 6 1870. 1090. 5.260 28.90 2.20 4600.000
2.56 1.85 9650 0.66800
U 3 0000 0000 0 0 00 0
000
157.
G 6 3539. 1585. 7.890 19.90 158. 48890.00
2.54 1.61 2500 0.95000
D 4 0000 0000 0 0 0000 00
000
158.
T 6 3496. 1630. 8.270 19.20 0.00
2.51 1.59 9253 0.73800 23.4000
B 5 0000 0000 0 0 40
400
 162.
D 6 2835. 1682. 8.540 19.00 54.5
2.49 1.59 5000 1.69000 940.0000
Y 6 0000 0000 0 0 000
000
164.
H 6 2968. 1743. 8.800 18.70 0.36
2.47 1.58 9303 0.80800 64.7000
O 7 0000 0000 0 0 00
200
167.
E 6 3136. 1795. 9.050 18.40 1.20
2.45 1.57 2600 0.80300 159.2000
R 8 0000 0000 0 0 00
000
168.
T 6 2220. 1818. 9.330 18.10 0.41
2.42 1.56 9342 0.70500 105.0000
M9 0000 0000 0 0 00
100
173.
Y 7 1467. 1097. 6.980 24.79 3.00
2.40 1.74 0400 1.24000 35.1000
B 0 0000 0000 0 0 00
000
174.
L 7 3668. 1936. 9.840 17.78 0.10
2.25 1.56 9670 0.73000 76.4000
U 1 0000 0000 0 0 00
000
178.
H 7 4876. 2500. 13.10 13.60 2.60
2.16 1.44 4900 0.77700 104.1000
F 2 0000 0000 00 0 00
000
180.
T 7 5731. 3287. 16.60 10.90 0.02
2.09 1.34 9479 0.69100 20.6000
A 3 0000 0000 00 0 00
000
183.
7 5828. 3680. 19.30 2.00
W 2.02 1.30 8500 9.530 0.47700 18.4000
4 0000 0000 00 00
000
186.
R 7 5869. 3453. 21.00 0.90
1.97 1.28 2070 8.850 0.92000 90.7000
E 5 0000 0000 00 00
000
190.
O 7 5285. 3300. 22.40 0.40
1.92 1.26 2000 8.490 1.10000 16.0000
S 6 0000 0000 00 00
000
192.
I 7 4701. 2716. 22.50 0.20
1.87 1.27 2200 8.540 1.06000 425.3000
R 7 0000 0000 00 00
000
195.
P 7 4100. 2045. 21.40 0.13
1.83 1.30 0800 9.100 0.96300 10.3000
T 8 0000 0000 00 00
000
 196.
A 7 3130. 1337. 19.30 10.20 0.36
1.79 1.34 9665 0.76300 98.6500
U 9 0000 5800 00 0 00
400
200.
H 8 630.0 234.2 13.53 14.82 6.70
1.76 1.49 5900 1.26600 372.3000
G 0 000 800 00 0 00
000
204.
T 8 1746. 577.0 11.85 17.20 0.14
2.08 1.48 3833 0.87850 3.4300
L 1 0000 000 00 0 00
000
207.
P 8 2023. 600.6 11.40 18.17 0.00
1.81 1.47 2000 0.94003 0.1710
B 2 0000 000 00 0 30
000
208.
B 8 1837. 544.5 9.800 21.30 0.00
1.63 1.46 9803 0.85256 0.0338
I 3 0000 200 0 0 72
700
209. -
P 8 1235. 527.0 9.400 22.23
1.53 1.46 0000 -0.01000 0.01 -0.0100
O 4 0000 000 0 0
000 00
210. - -
A 8 610.0 575.0 -
1.43 1.45 0000 0.010 -0.01000 0.01 -0.0100
T 5 000 000 0.010
000 0 00
222. -
R 8 211.0 202.0 9.910 50.50
1.34 1.43 0000 -0.01000 0.01 -0.0100
N 6 000 000 0 0
000 00
223. -
F 8 950.0 300.0 - 0.00
3.50 2.50 0000 0.010 0.84950 0.0360
R 7 000 000 0.010 72
000 0
226.
R 8 1809. 973.0 5.000 45.20 0.00
3.00 2.40 0250 1.00000 12.8000
A 8 0000 000 0 0 00
000
227. -
A 8 3473. 1323. 10.07 22.54
3.20 2.20 0280 -0.01000 0.01 -0.0100
C 9 0000 0000 00 0
000 00
232.
T 9 5061. 2028. 11.70 19.90 0.00
3.16 1.65 0381 0.98400 7.3700
H 0 0000 0000 00 0 00
000
231. - -
P 9 15.40 15.00 0.00
3.14 -0.01 0358 0.010 0.010 0.91000 200.6000
A 1 00 0 00
800 0 0
 238.
9 4407. 1405. 18.90 12.59 0.00
U 3.11 1.42 0289 0.84170 7.5700
2 0000 0000 00 0 40
000
237. -
N 9 910.0 20.40 11.62 0.00
3.08 -0.01 0480 0.010 1.05500 175.9000
P 3 000 00 0 00
000 0
244.
P 9 3503. 913.0 19.80 12.32 0.00
3.05 -0.01 0000 1.41000 558.0000
U 4 0000 000 00 0 00
000
243.
A 9 2880. 1268. 13.60 17.86 0.00
3.02 -0.01 0000 0.83000 75.3000
M5 0000 0000 00 0 00
000
247. -
C 9 1340. 13.51 18.28 0.00
2.99 -0.01 0000 0.010 0.70000 0.0000
M6 0000 10 0 00
000 0
247. - - - -
B 9 -
2.97 -0.01 0000 0.010 0.010 0.010 -0.01000 0.01 -0.0100
K 7 0.010
000 0 0 0 00
251. - - -
C 9 900.0 -
2.95 -0.01 0000 0.010 0.010 -0.01000 0.01 -0.0100
F 8 000 0.010
000 0 0 00
254. - - - -
E 9 -
2.92 -0.01 0000 0.010 0.010 0.010 -0.01000 0.01 -0.0100
S 9 0.010
000 0 0 0 00
1 257. - - - -
F -
0 2.90 -0.01 0000 0.010 0.010 0.010 -0.01000 0.01 -0.0100
M 0.010
0 000 0 0 0 00
1 258. - - - -
M -
0 2.87 -0.01 0000 0.010 0.010 0.010 -0.01000 0.01 -0.0100
D 0.010
1 000 0 0 0 00
1 259. - - - -
N -
0 2.85 -0.01 0000 0.010 0.010 0.010 -0.01000 0.01 -0.0100
O 0.010
2 000 0 0 0 00
1 260. - - - -
L -
0 2.82 -0.01 0000 0.010 0.010 0.010 -0.01000 0.01 -0.0100
R 0.010
3 000 0 0 0 00

Bibliography
1
D. Svergun, C. Barberato, and M. H. Koch,
CRYSOL - A program to evaluate x-ray solution scattering of biological
macromolecules from atomic coordinates,
J. Appl. Crystallogr. 28, 768-773 (1995).
2
R. D. FRASER, T. P. MACRAE, and E. SUZUKI,
IMPROVED METHOD FOR CALCULATING CONTRIBUTION OF SOLVENT
TO X-RAY-DIFFRACTION PATTERN OF BIOLOGICAL MOLECULES,
J. Appl. Crystallogr. 11, 693-694 (1978).
3
M. Y. PAVLOV and B. A. FEDOROV,
IMPROVED TECHNIQUE FOR CALCULATING X-RAY-SCATTERING
INTENSITY OF BIO-POLYMERS IN SOLUTION - EVALUATION OF THE
FORM, VOLUME, AND SURFACE OF A PARTICLE,
Biopolymers 22, 1507-1522 (1983).

About this document ...

Some Atomic Constants Data Table

This document was generated using the LaTeX2HTML translator Version 2002-2-1 (1.70)

Copyright © 1993, 1994, 1995, 1996, Nikos Drakos, Computer Based Learning Unit, University
of Leeds.
Copyright © 1997, 1998, 1999, Ross Moore, Mathematics Department, Macquarie University,
Sydney.

The command line arguments were:

latex2html -t 'HTML version of atomdb_doc' -html_version 4.0 -split 3 -
auto_navigation -reuse 2 -scalable_fonts -short_extn -local_icons -images -
math atomdb_doc.tex

The translation was initiated by Xiangyun Qiu on 2005-07-30

 Supported atomic (group) types for solution scattering calculations

 Hydrogen atoms in PDB entries
 Bibliography
 About this document ...

Xiangyun Qiu 2005-07-30