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IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 1 of 16
Status and developments in
BL13-XALOC at Alba
IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 2 of 16
Why XALOC
XALOC-BL13 beamline determines the 3D structure of macromolecules (proteins, ADN/ARN) using X-ray crystallography
0,1 mm
Detector
DifractòmetreOrienta la mostra
RobotPosiciona la mostra
MicroscopiFlux congelador a -173º C
IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 3 of 16
3. Solve a
Protein crystal
X-ray diffraction patternof protein crystal at the pixel detector
3D image at atomic resolution of a protein+DNA
IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 4 of 16
High demand
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34 Udays (29 proposals)
53 BT days
Cycle 1 (2012+) Cycle 2 (2013)
~50 proposals
• User Operation
97 BT days
IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 5 of 16
Beamline status
• Typical beam size at sample is 5010 um FWHM (HV) as seen on a 20-um fluorescence screen
• Unfocused and defocused modes were tested although not currently used.
• Very reliable beam optics (alignment done daily in 10’)
• Beam at sample drifts (typically downwards 1 um/hour)
• Beam recovered easily after a shutdown.
• Beam aligned using EH positioning tables. Optics (mirror pitches) could also be used.
• Measured beam flux is >2·1012 ph/s/250mA
Very positive comments from all (!) users
5010 m(FWHM, HV)
Beamline status : Operative (but not completed yet)
Flux
(ph
/s/2
50m
A)
E (keV)
#3#5
#7
#9
#11
#13
Underlying: diagnostics are very important
IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 6 of 16
Mono- chromator
Vertical Focusing Mirror
Dh = 5.4Dv = 3.47
Beamline description
Horizontal Focusing Mirror
Diffractometer
Sample changer
Detector
29.375
24.78522.800
20.100
Distance from source (m)
Beamline concept : In-vacuum Undulator IVU21.6 + Channel-cut Si(111) monochromator + KB focusing mirrors
ExperimentalHutch
Beamline status : Operative
IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 7 of 16
Monochromator
Vertical Focusing Mirror
Horizontal Focusing Mirror
Attenuator
FE trigger unit
Fluorescence screens
Diode XBPMs
Detector
Diffractometer
Sample changer
Slits
Photon shutter
Other optical elements
29.375 m
24.785 m
22.800 m
20.100 m
Dh = 5.4
Dv = 3.47
XALOC Layout
IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 8 of 16
• Channel cut Si(111), 6 mm gap, by CINEL (crystals by Crystal Scientific)• 5-22 keV, with 1 mm excursion (Pt-K →Se-K: 30 m; complete Se-MAD: 11 m)
cryogenic pipes
2nd xtal pitch (stepper motor)
2nd xtal pitchV feedback (piezo)
Bremsstrahlung block
channel cut crystal
Resolution Bragg Repeatability Bragg
1.10 ± 0.08 rad(0.064 mdeg)
2 rad monodirectional4 rad bidirectional
Measured at 1 full stepIn range 5-23 deg
Measures limited by thermal drift In range 5-23 deg
I0 diode
beam
accelerometer
Optics
IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 9 of 16
• 2 mirrors, in a Kirkpatrick-Baez configuration
• Manufactured by IRELEC, surfaces made by InSync
• Elliptically bent using 2 motors, equipped with strain gauges
• Equipped with accelerometers to monitor pitch vibrations
• Fully installed
Vertical Focusing Mirror
Horizontal Focusing Mirror
VFM HFM
Optical length 300 mm 600 mm
Stripes Si, Rh, Ir Si, Rh, Ir
Z Roll Pitch/Z
Range 10 mm 15 mrad 10 mm Tbd
Resolution 0.08 m 1 rad - TbdRepeatability 4 m 1 rad 1 m tbd
Optics: mirrors
IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 10 of 16
Lysozyme data set at Rsym (inner shell)<5%
• Test lysozyme crystal at 100K. • Excellent overall statistics: Rsym = 3.8 % (90 deg)• Also at the lowest resolution shell (2.76A): Rsym= 2 %.• Resolution 1.26 Å.• Molecular replacement rendered excellent ED maps.
lysozyme (a=b=79 Å c=37 Å; P43212)sample-det distance=200 mm=0.9795 Å, exp time =1 s, = 1°
High quality data: Lysozyme
• P3121 , a = b =31.5 Å, c = 106.8 Å• First data set collected at 12.6 keV and at 0.93 Å resolution:
0.5 deg oscillation, 90 deg, 1.3 sec exp timeRsym = 3.8 % (90 deg)
• Second data set collected at 15 keV and at 0.96 Å resolution: 0.5 deg oscillation, 205 deg, 2.6 sec exp time Rsym= 3.9 %
Atomic resolution data:T98D-SH3 domain of c-Src Tyr kinase
P3121 31.5 31.5 106.8Crystals from A. Cámara, UA, Almería
IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 11 of 16
Protein
DNA
• First ab initio solved structure, by Se K-edge SAD• Protein-DNA complex (PDB 2VS8)• Se-Met SAD 360˚, 2.4 Å resolution, 1 sec exp time
• P21, a = 106.6, b = 70.3, c = 107.1, = 119.9
Crystals from G. Montoya, CNIO, Madrid
SAD data collection: meganuclease I-Dmol D. Mobilis
Solve a structure using MAD at Se-K edge
Fluorescence scan widget
IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 12 of 16
• Monoclinic cell• a = 470 Å, b= 376 Å, c = 465 Å = 90˚, = 99˚, = 90˚• Diffraction to 4 Å.• Crystal-detector distance 750 cm (max. distance 1350 cm)
Human Rhinovirus 2
Crystals from N. Verdaguer, IBMB, Barcelona
Solve a structure with a unit cell par. a>400 Å
IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 13 of 16
Detectors at the Experimental Hutch
Pixel main detector
Fluorescence Si-drift detector
Diamond X-ray position monitors
PIN Diodesand YAG fluorescence
screens
IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 14 of 16
• Pilatus 6M (Dectris)• Photon counting pixel detector• Preliminary tests on integration into BL
successfully passed• Currently ending manufacturing phase• Estimated delivery in May 2011• Data transfer and storage system to be defined
Area 431 x 448 mm2
Pixel size 172 mPoint spread 1 pixel
Max. framing rate 12 Hz
Dynamic Range 20 bits (106 ct)
Usable count rate 2x106 cts/s
Energy trimming Yes, recommended E0/2Gain 3, Fast, standard, high
ALBA turn = 893 ns
124 ns
Detector
IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 15 of 16
• 320 um Silicon: needed thicker• Smaller pixel size• Tiling is tolerable, but gaps should be reduced• 2.3 ms dead time: can be smaller?• Area, area• Triggers, triggers, triggers
Area 431 x 448 mm2
Pixel size 172 mPoint spread 1 pixel
Max. framing rate 12 Hz
Dynamic Range 20 bits (106 ct)
Usable count rate 2x106 cts/s
Energy trimming Yes, recommended E0/2Gain 3, Fast, standard, high
ALBA turn = 893 ns
124 ns
Detector. What else?
?
?
IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 16 of 16
• Transmissive PIN diode• Collaboration with CNM• 10x10mm2• transmissive (10 um thick)
Other projects
• Pinhole• Heavy Z material, 80 um thick• Hole 3-20 um diameter
• Fluorescence dot• Mounted in a sample holder• 1 um diameter• Used to position beam and
spindle
• High precision tools• Sharp tips <1um• Slit blades
IFAE-Alba meeting | Alba, 13 december, 2012XALOC-BL13 17 of 16
Thank you for your attention
The XALOC Team
First data setApril 2012
First Official Users 18 July 2012
EngineeringCarles Colldelram Mech EngineerAlex Enrique Mech TechnicianFabien Rey AlignmentMarcos Quispe Cryogenics
ComputingGuifré Cuní Controls EngineerOscar Matilla Electronic EngineerJulio LidónXavi Fariña Elec technician
ExperimentsJordi JuanhuixJordi BenachFernando GilJ.C. Martínez metrologyJosep Nicolás mirrors, metrologyIgors Sics diagnostics