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PDBsum entry 2a7a
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Metal binding protein
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PDB id
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2a7a
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References listed in PDB file
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Key reference
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Title
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On the routine use of soft X-Rays in macromolecular crystallography. Part III. The optimal data-Collection wavelength.
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Authors
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C.Mueller-Dieckmann,
S.Panjikar,
P.A.Tucker,
M.S.Weiss.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2005,
61,
1263-1272.
[DOI no: ]
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PubMed id
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Abstract
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Complete and highly redundant data sets were collected at different wavelengths
between 0.80 and 2.65 A for a total of ten different protein and DNA model
systems. The magnitude of the anomalous signal-to-noise ratio as assessed by the
quotient R(anom)/R(r.i.m.) was found to be influenced by the data-collection
wavelength and the nature of the anomalously scattering substructure. By
utilizing simple empirical correlations, for instance between the estimated
deltaF/F and the expected R(anom) or the data-collection wavelength and the
expected R(r.i.m.), the wavelength at which the highest anomalous
signal-to-noise ratio can be expected could be estimated even before the
experiment. Almost independent of the nature of the anomalously scattering
substructure and provided that no elemental X-ray absorption edge is nearby,
this optimal wavelength is 2.1 A.
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Figure 1.
Figure 1
Estimated anomalous diffraction ratio [Delta] F/F in the wavelength range 0.5-3.0 Å
for the ten model systems described in this paper. The estimate is for zero scattering
angle and assumes resolved and independent anomalous scatterers. The ten systems are
separated into two groups (Xe group and P/S/Ca group) and sorted in decreasing strength of
the anomalous signal. Black lines, ConA-Xe, adaptin-Xe, PPE-Xe and HEL-Xe; blue line,
thermolysin; green lines, DNA, HEL, trypsin, thaumatin and PPE-Ca. The experimentally
determined anomalously scattering substructures for the ten systems were (1) ConA-Xe: two
protein S atoms, one Mn2+ and one Ca^2+ ion, both fully occupied, as well as six Xe atoms
with occupancies (q) of 0.40, 0.30, 0.20, 0.15, 0.15 and 0.10; (2) adaptin-Xe: four
protein S atoms and two Xe atoms (q = 0.32 and 0.10); (3) PPE-Xe: ten protein S atoms, one
Xe atom (q = 0.72) and two SO[4]^2- ions (q = 0.70 and 0.50); (4) HEL-Xe: ten S atoms, two
Xe atoms (q = 0.24 and 0.08), the first one being situated on a crystallographic twofold
axis, and eight Cl- ions (q = 0.68, 0.58, 0.52, 0.37, 0.37, 0.34, 0.31 and 0.28); (5) DNA:
eight P atoms; (6) HEL: ten S atoms and seven Cl- ions (q = 0.80, 0.77, 0.70, 0.60, 0.57,
0.37 and 0.25); (7) thermolysin: two protein S atoms, six Ca^2+ ions (q = 1.00, 1.00,
1.00, 1.00, 0.50 and 0.25), one fully occupied Zn2+ ion and two DMSO molecules (q = 0.50
and 0.40); (8) trypsin: 14 protein S atoms, one fully occupied Ca^2+ ion and two partially
occupied Cl- ions (q = 0.40 and 0.25); (9) thaumatin: 17 protein S atoms and (10) PPE-Ca:
ten protein S atoms, one Ca^2+ ion (q = 0.81) and one Cl- ion (q = 0.30).
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Figure 4.
Figure 4
Dependence of the observed R*[r.i.m] values on the data-collection wavelength. The data
distribution can be fitted with the exponential function R*[r.i.m] = 3.78 + 0.0002exp(3.76
[lambda] ) and an R2 value of 0.57. The three outliers (DNA data sets collected at
[lambda] = 2.10, 2.30 and 2.50 Å, respectively) not obeying the exponential fit are
shown as open circles.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2005,
61,
1263-1272)
copyright 2005.
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