Learn about the Disulfide Oxidoreductases

RapiData 2007 Pictures from the course

Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement

Biology Department and National Synchrotron Light Source
Brookhaven National Laboratory
22-27 April 2007

Course Agenda

Organized by: R.M. Sweet, S. Sclafani, H. Robinson, L. Berman, D. Schneider, A. Heroux, A. Saxena, and A. Soares

Sponsors:

This course is sponsored by a grant from the National Institute of Health National Center for Research Resources to the Brookhaven Biology Department and National Synchrotron Light Source, and in part by support from the Department of Energy Office of Biological and Environmental Research.

We also thank the International Union of Crystallography, Brookhaven Science Associates, Area Detector Systems Corp, Hoffmann - La Roche, Merck, Amgen, Bruker AXS, Bristol-Myers Squibb, Rigaku Americas, Hampton Research Corp., and MiTeGen for financial assistance for this course.

Saturday 21 April:

6 PM: Meet at Berkner Hall to go out for dinner. Bring a car if you have one.

Sunday 22 April:

Crystallographic Fundamentals.

Get breakfast at Berkner hall with your meal voucher.

9:00 AM: A day-long course will be given by R. Sweet from 9:00AM to roughly 3:30PM, with a mid-day break, to provide additional background to students whose experience might leave them a bit baffled by the lectures in the course. A wide range of fundamentals of diffraction theory, data production, data collection, and structure solving will be presented, with the focus being to provide prerequisite knowledge for the remainder of the course. The course will be in the Seminar room at the far East end of the Biology Department, Building 463, roughly I7 on the BNL site map.

3PM and after: All students and instructors who do not have a BNL ID should go to the NSLS Users' Office before 5PM to complete NSLS registration. Any who haven't done so, please take both the Safety and the Radiological modules of the NSLS safety training now. Students may complete their registration for RapiData and pick up course materials in Berkner Hall, G5 on the BNL site map.

5PM: Teachers who need to check electronic lecture materials may do that at the Biology lecture room.

5 - 7 PM: Supper at Berkner.

Monday 23 April:

7:15 AM: NSLS User Office will be open for any final registrations.

8:00 AM: Continental Breakfast at Biology Dept. seminar room (Far East End of the building, Bldg. No 463).

Lectures -- Biology Department:

8:30 Welcome and Introduction

8:45 Diffraction Geometry for the Rotation Method -- Bob Sweet (BNL)

9:30 Strategy vs tactics in data collection -- Zbyszek Dauter (NIH)

10:15 Coffee

10:30 Modern CCD-based x-ray detectors -- Chris Nielsen (Area Detector Systems Corp.)

11:10 Special properties of SR: polarization, bandwidth, collimation -- Lonny Berman (BNL)

11:50 Lunch -- In Medical Dept. Seminar Room

1:00 Data reduction with d*TREK -- Jim Pflugrath (Rigaku Americas)

1:45 Data reduction with the DPS/Mosflm Package -- Gordon Leonard (European Synchrotron Radiation Facility)

2:30 Coffee

2:45 Data reduction with the HKL suite -- Wladek Minor (U. Va)

3:30 Automatic control of data collection with the "dna" and xia2 systems -- Graeme Winter (Daresbury)

4:10 Head to the NSLS

Visit to the NSLS:

4:20 Quick walking tour of the NSLS.

5:15 Drinks and conversation at Berkner.

6:15 Dinner

7:30 - 9:30 Back to NSLS for tutorials and conversation. Groups A-F check your crystals!!

Tuesday 24 April

8:00 Breakfast in Biology Dept.

Lectures -- Biology Dept.:

8:30 Cryocooled specimen preparation for the synchrotron -- Allen Orville (BNL)

9:15 Are we MAD or are we SAD? -- Howard Robinson (BNL)

10:00 Structure solving with SHELX -- Matt Benning (Bruker AXS)

10:45 Coffee

11:00 Structure solving with SOLVE and Phenix -- Tom Terwilliger (LANL)

11:45 Structure solving with autoSHARP -- Claus Flensburg (Global Phasing)

12:30 Lunch -- In Medical Dept. Seminar Room

1:15 Structure solving with Molecular Replacement methods -- Paul Adams (LBL)

2:00 Operation of beam line software: CBass, PXDB -- John Skinner (BNL)

2:30 Head to the NSLS

Laboratory work -- NSLS

2:40 Coffee, etc. available at X8 and the blue cubicle near X20

2:50 Introduction to the beam lines at the beam line -- Individual instructors

Beam line Operations and Safety Awareness Training
Creation of the SAF for the two groups at each beamline

Demonstration of Specimen mounting and test shots

3:45 - 4:00 Begin beam line Meetings: Groups meet with beam line staff to discuss projects and to prepare a schedule for data-collection.


Beamline	X4-A	X8-C	X3-A	X12-B	X12-C	X26-C
Mtg. Room Safety Form	Seminar Room	X8 Conf. Room	X8 Conf. Room	X12 Cyber Café	Blue cubicle near X20	Library

Check on group assignments here: Web Page or Excel Spread Sheet

Check on computer information for the course.

5:45 Drinks and conversation at Berkner

6:15 Dinner

7:30 - 9:30 Back to NSLS for tutorials, start of data collection, and conversation.
The x-tal prep room will be open with Allen Orville and Dan Thiel in attendance.

Beam line configuration (Beam line labels are selectable here -- have a look at beam line documentation):

Beamline X4-A
X8-C X3-A X12-B
X12-C X26-C

Morning Startup Schwanof
Flaks Babu Soares
Saxena Heroux

Software HKL2000 DPS/Mosflm HKL2000 dna/Mosflm d*TREK DPS/Mosflm

Helpers Klei
Abramowitz
Szebenyi
Birktoft
Dauter
Shi
Zwart
Rould
Raji E Nielsen
Pflugrath
Enemark
Thibault

Beamline	X4-A	X8-C	X3-A	X12-B	X12-C	X26-C
Morning Startup	Schwanof	Flaks	Babu	Soares	Saxena	Heroux
Software	HKL2000	DPS/Mosflm	HKL2000	dna/Mosflm	d*TREK	DPS/Mosflm
Helpers	Klei Abramowitz	Szebenyi Birktoft	Dauter Shi Zwart	Rould Raji E	Nielsen Pflugrath	Enemark Thibault

Group assignments and very rough data-collection schedule:

Time X4-A
X8-C X3-A X12-B X12-C X26-C X-tal prep. and tutorials

Tues 8 PM A B C D E F G-L

Wed 2:00 PM G H I J K L A-F

Thurs 8AM A B C D E F G-L

Thurs 8PM G H I J K L --

Time	X4-A	X8-C	X3-A	X12-B	X12-C	X26-C	X-tal prep. and tutorials
Tues 8 PM	A	B	C	D	E	F	*G-L*
Wed 2:00 PM	G	H	I	J	K	L	*A-F*
Thurs 8AM	A	B	C	D	E	F	*G-L*
Thurs 8PM	G	H	I	J	K	L	--

Wednesday - Thursday 25-26 April:

8:00 AM: Breakfast in NSLS Library

Data Collection Sessions and tutorials, including crystal preparation at X12, will run concurrently throughout the day. There will be sign-up sheets for all of the tutorials.

Noon: Lunch in NSLS Library

3:30 PM: There will be a required meeting in the NSLS Seminar Room both afternoons at 3:30 to compare notes and make announcements.

6:00 PM: Supper in NSLS Library

Friday 27 April:

Recapitulation -- Biology Dept.

8:00 Breakfast in Biology

8:30 The course staff, with the help of students, will recount triumphs, troubles, and interesting observations. Course staff will be available until noon to assist students in tidying up calculations, backing up data, etc.

Version of 19 April 2007