Building a user-friendly beamline

Aina Cohen and Paul Ellis

PDB structures May-July ’03

HOME SOURCES SYNCHROTRONS

MR v. PHASE MEASUREMENT

MOLECULAR

REPLACEMENTEXPERIMENTAL

PHASES

EXPERIMENTAL PHASING

MIR

SIR

MAD

SAD

AB INITIO

ANOMALOUS SCATTERERS

ANOMALOUS SCATTERERS

Optimised sulfur anomalous

Xenon anomalous

ANOMALOUS SCATTERERS

ANOMALOUS SCATTERERS

ANOMALOUS SCATTERERS

ANOMALOUS SCATTERERS

Krypton & Xenon

► Underutilized

► Tend to be relatively isomorphous

► Must be stable in cryoprotectant

► Good chance of useful derivative

► Quillin: large-to-small mutations

Kr Xe

“on” rate fast slow

“off” rate fast slow

binding weaker stronger

MAD? yes (K) no

ANOMALOUS SCATTERERS

Derivatizing with quick soaks

► Quick soaks can be much less time consuming than traditional long soaks or cocrystallizing

► High concentrations can be destructive of crystal order

► Ions used include:– Br-, I-

– Cs+, Rb+

– Sr2+

– Gd3+, Ho3+, Sm3+, Eu3+

“traditional” “quick”

heavy atom concentration mM M

soaking time ≥ hours ≤ minutes

ANOMALOUS SCATTERERS

ANOMALOUS SCATTERERS

Beamline parameters

To cover the great majority of samples:

» ?

Beamline parameters

To cover the great majority of samples:

» Energy range: <6-17 keV

Beamline parameters

To cover the great majority of samples:

» Energy range: <6-17 keV

» Fast energy moves

Beamline parameters

To cover the great majority of samples:

» Energy range: <6-17 keV

» Fast energy moves

» Resolution: ~1 eV

Beamline parameters

To cover the great majority of samples:

» Energy range: <6-17 keV

» Fast energy moves

» Resolution: ~1 eV

» Spot size: 250 µm - <50 µm

SSRL BL9-2

+ Good Flux+ Useful Energy Range (6-16 keV)+ Rapid Energy Changes

BL9-2 Oversubscribed

What Else Do We Have?

What Else Do We Have?

9-1 & 11-1

9-1: 12500-16500 eV

11-1: 10500-15000 eV

(9-2: 6000-16000 eV)

+ Good flux+ Access to useful energy ranges

-- 15 minutes to 1/2 hour at best to change energy

Energy Moves at Side Stations

To change energy at BL9-1 or BL11-1the following must be repositioned:

monochromator theta table slide (theta)monochromator bend table vertical table pitch

table horizontal table yaw

Weight (kg)

Q315 detector: 140Positioners: ~340Goniometer: ~70Robotic Mounting System: ~90Counter Weight: 72Other Devices: ~45Tabletop: 225

Total - ~ 1000 kg

Energy Tracking Requirements:

To change energy from 12500 eV to 16500 eV, the experimental table at BL9-1 must move almost a meter (as measured from the end of the table).

The mechanical components must be highly reproducible (better than 50 µm).

Most of the effort to implement this system was in trouble-shooting and replacing components that were not to spec.

Reliable Computer Controlled Positioners

Energy Tracking Requirements:

Advanced Hardware Control System (DCSS)

Beam LineOptics

ExperimentalHardware

DetectorSystem

Fl. DetectorSensor A/D

DHSNT

DHS VMS

Galil

Galil

Distributed Control System Server (DCSS)Central Database / Scripting Engine

BLU-ICE GUI SGI

BLU-ICE GUI SGI

BLU-ICE GUI linux (remote)

Galil

Galil

Galil

DHS linux

DHS SGI (fileserver)

Fit these values to a polynomial function of monochromator theta.

Creating the DCS script

0

100

200

300

400

500

600

700

800

900

13 14 15 16 17 18

Slide Measured

Slide Calculated

-250

-200

-150

-100

-50

0

50

100

150

200

250

0 100 200 300 400 500 600 700 800 900

Optimize the beam line at different energies and record the motor positions

Table Slide Position (mm) verses Monochromator Theta

Difference Between Measured and Calculated Table Slide Positions (microns)

TableSlide =

– 2052.82

+ MonochromatorTheta x 165.354

– MonochromatorTheta2 x 0.219763

Write a Tcl/Tk script

Typical Se Edge Scans

BL9-1

BL9-2

The Results

Further Automation of MAD Data Collection

Reliable Computer Controlled Hardware Advanced Control System (DCS) +

The Scan Tab

Automated MAD scans

What bottlenecks remain?

Sample Mounting

- Hutch access is time consuming- Crystals commonly lost due to human error- Data often not collected from the best crystal

Data Collection

- Detector Readout Time- Exposure Times of 10 seconds or more

Unreliable Hardware

- Difficult to maintain and trouble-shoot- Increases alignment time- Frequent break downs

SSRL Crystal Mounting System

Cassette Stores 96 Samples

Mount 3 cassettes at the beam line

• Ship 2 cassettes inside a Taylor Wharton or MVE dry shipper•

Store 20 cassettes inside a Taylor Wharton HC35 storage device

NdFeB ring magnet

Standard Hampton pins

The Dispensing Dewar

Vertically opening gripper arms

The Robot and Gripper Arms

Z

U

θ1

θ2

Fingers to HoldDumbell Magnet Tool

Cryo-tong Cavity

Epson ES553 Robot

Robot Demonstration

Crystal screening tab in BLU-ICE

Cassette Tool Kit Supplied

(A) Sample Cassette and Hampton pins

(B) Alignment Jig – to aid mounting pins into cassettes

(C) Transfer Handle – for handling cold cassettes

(D) Magnetic Tool – to mount pins in cassette & to test pin size

(E) Dewar Canister – replaces stock canister in dry shipping dewars

(F) Styrofoam Spacer – keeps single cassette in place when shipping

(G) Teflon Ring – to support the canister in the shipping dewar

Styrofoam box holds liquid nitrogen for loading cassettes

Cassette Tool Kit Demonstration

Vertically opening gripper arms

Force Sensor

Fingers to HoldDumbell Magnet Tool

Cryo-tong Cavity

Force Sensor

Automated Calibration

View of the Robot System on 1-5, 9-1, 9-2 and 11-1

9-1

1-5

9-2 9-1

11-1

11-3

+ 3x3 array of CCD modules

+ Active area of 315 x 315 mm

+ 51 micron pixel size

One Second Readout

ADSC Quantum-315 at BL9-2, BL9-1, BL11-1 &

coming to BL11-3

This readout speed is 10 times faster

than the Quantum-4

Beam Line 11-1 11-3 9-2 9-1 7-1 1-5

Relative Intensity SPEAR 40X 15X 20X 15X 7X X

Relative Intensity SPEAR3 200X 75X 200X 75X 35X 100X

Wavelength Range (Å) 0.82-1.2 0.97-0.98 0.62-2.1 0.73-0.99 1.08 0.77-2.1

Energy Range (keV) 10.5-15 12.6-12.8 5.9-20 12.5-16.5 11.5 5.9-16

Detector Readout (sec) 1 1 1 1 40-90 10

Detector Size (mm) 315 315 315 315 180-345 188

SPEAR3

The relative intensities of the SMB crystallography beamlines (~1 Å and 0.2 mm collimation) for the current SPEAR at 100 mA (measured) and for SPEAR3 at 500 mA (estimated).

Unreliable Hardware

New Final Beam Conditioning System

New Final Beam Conditioning System

150 mm

75 mm

Solutions

Sample Mounting with SSRL Robotic System

+ Screen up to 288 crystals without entering the experimental hutch+ Feedback systems and calibration checks ensure reliable operation+ Many crystals are quickly screened and data collected from only the best

Data Collection Times Reduced

+ 1 second readout + higher intensities + better focus

Upgraded Final Beam Conditioning System

+ Modular design enables rapid replacement of broken components + easy to maintain - compact, few cables, He tight + increased functionality, and feed back

Where do we go from here?

• Automated data collection from the best crystals • Automatic structure solution• Sample tracking database• More feedback• Automated beam line alignment and calibration

Remote Access

The Macromolecular Crystallography Group

Department of Energy, Office of Basic Energy SciencesDepartment of Energy, Office of Basic Energy Sciences

The Structural Molecular Biology Program is supported by:The Structural Molecular Biology Program is supported by:

National Institutes of Health, National Center for Research National Institutes of Health, National Center for Research Resources,Biomedical Technology ProgramResources,Biomedical Technology Program

NIH, National Institute of General Medical SciencesNIH, National Institute of General Medical Sciences

and by the and by the

Department of Energy, Office of Biological and Environmental Research.Department of Energy, Office of Biological and Environmental Research.

SSRL DirectorKeith Hodgson

SMB LeaderBritt Hedman

MC LeaderMike Soltis

Günter Wolf, Scott McPhillips, Paul Ellis, Aina Cohen, Jinhu Song, Zepu Zhang, Henry Van dem Bedem, Ashley Deacon, Amanda Prado, Jessica Chiu, John Kovarik, Ana Gonzalez, John Mitchell, Panjat Kanjanarat , Mike Soltis, Hillary Yu, Ron Reyes, Lisa Dunn, Tim McPhillips, Dan Harrington, Mike Hollenbeck, Irimpan Mathews, Joseph Chang, Irina Tsyba, Ken Sharp, Paul Phizackerley

Ideal Hampton Pin Lengths for Cassette

Hampton Mounted CryoLoop in a MicroTubeHampton Mounted CryoLoop in a MicroTube

Hampton CrystalCap Magnetic Hampton 18mm CrystalCap Copper Magnetic

Carrier for Two Modified ALS “Pucks”

Carrier that Mountsin place of CassetteIn Dispensing Dewar

ALS Puck withSSRL-style RingMagnets Inside

ALS Tapered Pin