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The high photon flux at third-generation synchrotron sources can inflict significant primary radiation damage upon macromolecular crystals, even when the crystals are cryocooled. However, specific radiation-induced structural changes can be exploited for de novo phasing by an approach known as radiation damage-induced phasing (RIP). Here, RIP and single-wavelength anomalous dispersion (SAD) phasing were alternatively used to derive experimental phases to 1.2 Å resolution for crystals of an α-helical 18-residue peptide, MINTS, which was derived from the neurotoxin apamin and the palladium-bound structure of which is now reported. Helix formation is induced by the binding of palladium (or copper) to two histidines spaced four residues apart, while two disulfide bonds tether the N-terminal helix to the C-terminal loop-like part of the peptide. Either RIP or SAD phasing of the palladium-bound and copper-bound forms of MINTS, which crystallized in different space groups, resulted in density maps of superb quality. Surprisingly, RIP phasing of the metal-bound complex structures of MINTS was a consequence of differential radiation damage, resting primarily on the reduction of the disulfide bonds in Pd-MINTS and on depletion of the metal sites in Cu-MINTS. Its miniprotein-like characteristics, versatile metal-binding properties and ease of crystallization suggest MINTS to be a convenient test specimen for methods development in crystallographic phasing based on either synchrotron or in-house X-ray diffraction data.

Supporting information

pdf

Portable Document Format (PDF) file https://doi.org/10.1107/S0907444907065948/hv5095sup1.pdf
Supplementary material

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0907444907065948/hv5095sup3.cif
Contains datablocks global, PD-MINTS

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0907444907065948/hv5095sup2.hkl
Contains datablocks refine_set, phasing_set

CCDC reference: 681217

Computing details top

Cell refinement: XSCALE; program(s) used to solve structure: SHARP; program(s) used to refine structure: REFMAC 5.2.0019.

(PD-MINTS) top
Crystal data top
?β = ?°
Mr = ?γ = ?°
?, ?V = ? Å3
a = ? ÅZ = ?
b = ? Å? radiation, λ = ? Å
c = ? Å × × mm
α = ?°
Data collection top
h = ??l = ??
k = ??
Refinement top
Crystal data top
?β = ?°
Mr = ?γ = ?°
?, ?V = ? Å3
a = ? ÅZ = ?
b = ? Å? radiation, λ = ? Å
c = ? Å × × mm
α = ?°
Data collection top
Refinement top

Experimental details

Crystal data
Chemical formula?
Mr?
Crystal system, space group?, ?
Temperature (K)?
a, b, c (Å)?, ?, ?
α, β, γ (°)?, ?, ?
V3)?
Z?
Radiation type?, λ = ? Å
µ (mm1)?
Crystal size (mm) × ×
Data collection
Diffractometer?
Absorption correction?
No. of measured, independent and
observed (?) reflections
?, ?, ?
Rint?
Refinement
R[F2 > 2σ(F2)], wR(F2), S ?, ?, ?
No. of reflections?
No. of parameters?
No. of restraints?
Δρmax, Δρmin (e Å3)?, ?

Computer programs: XSCALE, SHARP, REFMAC 5.2.0019.

 

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