SHELX WORKSHOP MONTREAL
ARCIMBOLDO and
Macromolecular crystallography
limited resolution: derived from less perfect crystals
containing 50% solvent
BORGES for solving
Predictable structures or building blocks
macromolecules ab
Phasing is a bottleneck solved by
initio
Derivatives: MAD, SAD, SIR, SIRAS, RIP
Molecular replacement
Isabel Usón
Ab initio: solve the structure from the native intensities
alone, without derivatives or particular previous
structural knowledge.
ICREA, IBMB-CSIC
[email protected]
Dual space recycling
in SHELXD
The real space part of the
cycle imposes a strong
atomicity constraint on the
phases that are then refined
in the reciprocal space part.
CC is the correlation coeff.
between Eobs and Ecalc. For
data to atomic resolution
(1.2Å or better), CC > 65%
almost always indicates a
correct solution.
Structures solved by SHELXD
Fragment
Compound
Spacegroup
N(+solv)
Actinomycin X2
Actinomycin Z3
Vancomycin
Actinomycin D
Ristocetin A
Hirustasin
Cyclodextrin
Decaplanin
PolyA RNA
Cyclodextrin
Bucandin
Amylose CA26
Viscotoxin B2
Mersacidin
Feglimycin
Tsuchimycin
rc-WT CvHiPIP
Cytochrome c3
P1
P212121
P43212
P1
P21
P43212
P21
P21
P41212
P1
C2
P1
P212121
P32
273(305)
186(307)
2Cl
202(312)
6Cl
270(314)
294(420)
402(467)
10S
448(467)
448(635)
4Cl
478(572)
22P
483(562)
516(634)
10S
572(719)
722(812)
12S
750(826)
24S
P65*
828(1026)
P1
1069(1283)
1264(1599)
8Fe
2024(2208)
8Fe
P212121
P31
HA
dÅ
0.9
0.96
1.09
0.94
1.03
1.2
0.88
1.00
1.00
1.00
1.05
1.1
1.05
1.04
1.10
24Ca 1.00
1.2
1.2
Objective: to break the atomic
resolution dependency: 1.2-2Å
ARCIMBOLDO: enforce secondary
structure rather than atomicity
http://chango.ibmb.csic.es/ARCIMBOLDO
At lower resolution, constraints to replace atomicity:
fragments
ARCIMBOLDO (2.0 Å) combines
A small perfect substructure to seed phasing
fragment search (PHASER, Read)
Multisolution to span stages where a solution cannot
be identified
density modification/auto tracing
(SHELXE, Sheldrick) Multisolution:
Condor /SGE / TORQUE Grid /
Supercomputer
Figure of merit?
Instead of atom picking: density modification
Kay Diederichs, Steinbruch Centre for
Computing (KIT-SCC)
Exploit stereochemistry: autotracing (CC TRACE)
ARCIMBOLDO-LITE on 4J5M
[GENERAL]
working_directory= /path/to/workdir
mtz_path: %(work_directory)s/data.mtz
hkl_path: %(work_directory)s/data.hkl
[ARCIMBOLDO]
name_job: myo5b
f_label: FP
sigf_label: SIGFP
molecular_weight: 45635
number_of_component: 1
fragment_to_search: 3
helix_length: 22
[LOCAL]
# requires PHASER 2.5.6
path_local_phaser: phenix.phaser
path_local_shelxe: shelxe
Data 4J5M: Nascimento et al. 2013 J. Mol. Biol. 288, 34190-34204
ARCIMBOLDO: fragment location +
density modification
Small model
or known
substructure
Fragment
location with
PHASER
Add next
fragment
CC trace
Solution?
ARCIMBOLDO
Rodríguez, Sammito, Meindl, M de
Ilarduya, Potratz, Sheldrick & Usón
(2012),
Acta Crystallogr. D68, 336-343
Improve
solution
Density
modification,
mainchain
trace SHELXE
Header
Help 2
Help 1
Input .bor and how to run
ARCIMBOLDO
Output .html
ARCIMBOLDO_SHREDDER
ARCIMBOLDO_BORGES
Data from
Sp. group
NRES FRAG
D(Å)
P. Czabotar
P3121
120
1.30
1H14
M. Graille (4LUN)
P21
310
1H16
1.45
C. Tisné
P212121
130
LITE 2H14
1.5
X.Gomis-Rüth
P212121
560
Clustering shreds
1.5
K. v Hecke
P432
165
2H14
1.6
J. Hermoso
J. M. Pereda (4GDO)
D. C. Hissa, K. Gruber (4K82)
K. Zeth, A. Lupas (4GN0)
P61
C2
P21
P21
50
240
204
428
1H10
Composite frags 2H17
2H14
Composite frags 2H16
1.7
1.70
1.70
1.7
1.75
S. Trakhanov
P212121
144
1H14
V. Arcus (4E1P)
P21
112
2H12
1.8
CMI K. Zeth (4AEQ)
C2221
90
1H12
1.9
T. Pavkov
P41212
111
H13
1.9
R. Bunker (4BJS)
P1
240
Model helices
1.94
PRD2 S. Becker (3GWH)
P21
222
3H14
1.95
HellD Thorn, Sheldrick (3SZS)
I422
327
2nmr31
1.95
Van Breuguel
P21
600
Composite frags 2H17
1.97
MltE J. Hermoso (2Y8P)
C2221
378
shredder
2.0
X. Gomis-Rüth (4IJA)
P212121
794
Frags + Se-MAD
2.0
Nuria Verdaguer
P6322
50
3H14
2.1
ARCIMBOLDO-LITE on a
structure from C. Tisné
P212121, 134 aminoacids, 1.5 Å solved at U.
Descartes, Paris, with ARCIMBOLDO_LITE
AMPLE: Bibby J et al. (2012)
Acta Crystallogr D68, 1622-31.
SUPERCOMPUTER /
GRID/CLUSTER
Implementation on
a single
workstation
(MySQL database)
Supercomputer
Workstation:
Data, Output
Configure with
access data (user,
password, key)
Sends all heavy
calculations out
Condor GRID
SGE Cluster
MySQL
database
MOAB /Torque
CRI4 @ Structural Biology, IBMB-CSIC
Acknowledgements
George Sheldrick, Airlie McCoy and Randy Read, Kay
Diederichs
European and Brazilian tax-payers, Volkswagenstiftung