Policy Statement

Information and Operating Policy for the

NATIONAL MAGNETIC RESONANCE FACILITY AT MADISON

Biochemistry Department
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI 53706-1544

Primary contact person:
Rita Hannah, Ph.D.
Tel: (608) 262-3173
Fax: (608) 262-3759
E-mail: rhannah@nmrfam.wisc.edu

Dr. Hannah can answer questions about the facility and direct calls or e-mail to Dr. John L. Markley (head and PI) markley@nmrfam.wisc.edu or Dr. W. Milo Westler milo@nmrfam.wisc.edu (director).

Overview:
The National Magnetic Resonance Facility at Madison (NMRFAM) supports applications of nuclear magnetic resonance (NMR) spectroscopy to biochemical and biological systems, in particular to structure-function studies of biomacromolecules. The facility contains high-field, state-of-the-art NMR spectrometers for data collection and computers for processing and analyzing NMR data. The facility is staffed by experts in various fields of NMR experimentation who carry out core research and development and spend part of their time consulting with and training users. NMRFAM staff may collaborate with users who have projects of mutual interest. The web site www.nmrfam.wisc.edu; has information on the status of instruments, frequently asked questions, and protocols in use at NMRFAM.

Research emphasis:
The research focus of the facility is the important areas of (1) fast data collection and automated data analysis, (2) technology for larger proteins and complexes, (3) investigations of metal-containing (paramagnetic) proteins, (4) dynamics of macromolecules, and (5) structure-function investigation of RNA molecules and their complexes with metal ions and proteins.

By pursuing its innovative research technology development activities and by applying them to collaborative projects of biological importance, NMRFAM strives to be a model for demonstrating the future capabilities of the biomolecular NMR field. NMRFAM offers start-to-finish support for biomedical NMR investigations. As needed, NMRFAM will lend support to one or more of the following steps: (1) strategy evaluation, (2) sample preparation, (3) feasibility studies, (4) data collection, and (5) data analysis and structure determination. Our aim is to facilitate the efficient pursuit of new knowledge by providing researchers with resources matched to their particular needs. NMRFAM provides young investigators and experienced spectroscopists access to state-of-the-art instrumentation with support for multiple modes of data collection.

Protocols, pulse sequences, and software tools developed through NMRFAM’s research activities are made available to the general scientific community. The aim is to develop and disseminate advanced approaches to experiment design and data analysis that cover all steps in a biomolecular NMR investigation, from cloning through data deposition. With the goal of broadening the scope of its scientific activities, NMRFAM host distinguished visiting scientists working in areas related to its research technology development projects. As a means for training its user base and for disseminating its novel technology, NMRFAM conducts workshops and group training sessions; these are announced on the website.

Biomolecular NMR spectroscopy is the single approach that offers the most detailed information about biomolecules in solution, the milieu in which they normally function. NMR employs increasingly advanced technology to determine structures and to discover how biological systems work and respond to drugs. Our goal is to develop methods for making these investigations faster and less costly as well as applicable to larger classes of proteins and nucleic acids of importance in human disease.

NMR spectrometer systems
900 MHz (21.1T/54 mm) Varian DirectDrive NMR spectrometer with ¹H-detection triple-resonance ColdProbe
800 MHz (18.8T/63 mm) Varian DirectDrive NMR spectrometer with ¹H-detection triple-resonance ColdProbe
750 MHz (17.6 T/ 52 mm) Bruker DMX NMR spectrometer with ¹H-detection triple-resonance CryoProbe (with cold ¹³C preamp)
600 MHz (14.1T/51 mm) Varian DirectDrive NMR spectrometer with ¹H-detection triple-resonance ColdProbe and with automated sample changer
600 MHz(14.1T/51 mm) Varian DirectDrive NMR system spectrometer with ¹H-detection triple resonance cold probeÂ
600 MHz Bruker DMX NMR spectrometer (14.1 T/ 52 mm) with ¹H-detection triple-resonance CryoProbe
600 MHz Bruker DMX NMR spectrometer (14.1 T/ 52 mm) with ¹H-detection triple-resonance CryoProbe
500 MHz Bruker DMX NMR spectrometer (11.7 T/ 52 mm) with ¹H-detection triple-resonance CryoProbe
500 MHz Bruker Avance III NMR spectrometer (11.7 T/ 52 mm) with ¹³C,¹⁵N {¹H} CryoProbe (optimized for ¹³C and ¹⁵N observation) and 2 receivers
400 MHz (9.4 T/ 89 mm) Bruker DMX NMR spectrometer the main probe is a ¹H ¹³C ¹⁵N QNP with an assortment of standard probes and a surface coil probe.

All consoles have variable temperature ²H lock, pulsed field gradient, and shaped pulse capability. All Varian spectrometers have been upgraded to the Varian NMR system DirectDrive console. Each NMR system is connected to the Internet for communication and data transfer.

Data storage, analysis, and display:

NMRFAM computer systems:

Computers are available at NMRFAM for NMR data processing, analysis, structure calculations, and quantum mechanics. Nine rack mounted Supermicro servers: two 3 GHz dual core Pentium D that are assigned as the entry points through the firewall to the facility network via the secure shell, ssh; Two 5 TB RAID 10 (total space 24 TB) system for home directories and working space data storage; two 2 GHz 4Xquad core AMD Opteron (Barcelona) compute servers with 32 GB memory and 1 TB RAID 1 system; one 2 GHz 4X6 core Xeon compute server with 48 GB memory and 1 TB RAID 1 system; two 1.5 TB RAID 5 systems for backup of spectrometer data (currently this function is carried out by 2 DAT tape juke boxes); a 2 X dual core AMD system that acts the compute server for the PINE web server; and a 2 X quad core AMD system for administrative purposes. All of these computers run the CentOS or Fedora Linux operating system. Other NMRFAM computers include two SGI Altix 3300 compute servers each with 12 Intel 1.3 GHz Itanium 2 processors. Each machine has a total of 27.5 GB of main memory. Both systems are equipped with a 1 TB Fiber RAID for data storage. These systems are running SGI Advanced Linux server OS.

A variety of workstations: Four Dell 3×0 workstations running RedHat Linux serve as Varian spectrometer console hosts. Five SGI O2 systems running IRIX 6.5 serve as Bruker spectrometer console hosts. One Dell 390 running spectrometer softare serves as an offline data station. 16 O2s (R5K, R10K, R12K) and 5 Octanes (R10K with SI or SSI graphics). These machines run IRIX 6.5. Two Sun Microsystems workstations running Solaris 8 or 9. Numerous other diverse species of computers are part of the NMRFAM network.

Networking: The NMRFAM network infrastructure consists of 10/100/1000 Gb or 10/100 Mb Hewlett-Packard network switches and a 11 Mb wireless access point in the computer suite (Rm. B160). A 1 GB stwich links the Supermicro servers. Users can archive data on CD or DVD. Data can be transferred over the network to and from the facility.

Available NMRFAM software:

Software developed in-house includes:

PINE PINE is a suite of programs that incorporate:

PISTACHIO – probabilistic automated assignments

PECAN – probabilistic secondary structure prediction from NMR data

LACS – method for checking protein NMR datasets for anomalous chemical shift values or potential referencing problems

HIFI-NMR – A rapid data collection method is currently being incorporated in to the PINE suite

These software packages are available to all through a webserver accessed from the NMRFAM home page. Software for the implementation of rapid data collection methodology (HIFI-NMR) is available on NMRFAM spectrometers. Pulse programs and other software developed as NMRFAM are freely available for research purposes, either by distribution or from efficient local servers.

In addition to the NMR instrumentation described above, NMRFAM makes its computational resources available to users. Software packages from both commercial and academic sources are available for the analysis of NMR data, computation of structures, and quantum mechanical calculations. Programs installed on the NMRFAM compute servers systems include: nmrPipe, X-Plor-NIH, vmd-xplor, CYANA, UNIO_08 (ATNOS/CANDID,) Amber 9, Dock 5, HADDOCK, CARA, Gaussian 2003, Parallel Quantum Systems software, NBO 5, and Octave 3.0.

User laboratory:
A small laboratory is available to outside users of the facility. Its equipment includes a pH meter, NMR tube centrifuge, lyophilizer, refrigerator and freezer, fume hood, and balance. Desks and workstations are available for short-term visitors, and an office is available for longer-term visitors.

Access:
Resources of the facility are available at a modest fee (see below) to academic as well as industrial researchers. Allocation of service time on the instruments is based on the scientific merit of the project and its appropriateness to the mission of the facility as determined by peer review by NMRFAM and its Advisory Committee.

Technical assistance and training:
Persons who make extensive or non-routine use of the facility are encouraged to gain hands-on experience with the instruments so they can obtain and process data independently; members of the facility staff train these major users in the operation of the spectrometers.
Spectrometers can be operated remotely over the web by qualified operators.

Training can be requested by prior arrangement with NMRFAM staff members. New users who have signed up for data collection time can arrange for up to eight hours of training (usually over multiple sessions) free of additional charge over the normal spectrometer user fees. Additional training is available at the normal “operated-assisted” rates.

Collaboration:
NMRFAM instrumentation may be used independently and with “no strings attached.” However, a project that will make extensive use of facility staff or will require development of new experimental protocols should be arranged as formal collaborations backed up by letters of collaboration; co-authorship of publications is by mutual consent with knowledge and agreement of all authors prior to submission of manuscripts.

Routine spectroscopy service:
Routine spectra can be obtained and analyzed by facility staff on a service basis. Staff members are available for consultation on experiment design and training in data acquisition and processing. Application forms may be obtained from Dr. Rita Hannah or downloaded from the NMRFAM web site at http://www.nmrfam.wisc.edu/Documents/serv_req.txt.

Scheduling:
(1) Spectrometers.
Time requests are to be submitted one month in advance through the web-based booking software < www.sesame.wisc.edu/Sundial/sundial_main.html >. Requests are due by 4:00 pm on the 19th of the month prior to the requested time. If the 19^th falls on a Saturday, requests are due by 4:00 pm on Friday the 18^th. If the 19^th falls on a Sunday, requests are due by 4:00 pm on Monday the 19^th. Late requests will be given lowest scheduling priority. Principal investigators first register with NMRFAM and issue permits to members of their group; this allows individual group members to make time requests. The time request forms are designed to capture information needed to ensure that the proper instrumentation, software, and assistance is available to the user. Additional information is collected to be used for the facility’s reporting obligations to the granting agencies. Interactive current schedules (users can sign up for empty blocks of time), details, and help are available through Sundial.

For high demand instruments, the combined time requested by all users may be greater than what is available that month. NMRFAM will do it’s best to accommodate all users, either on the requested instrument or an alternative spectrometer. However, some users may need to be deferred until the following month. A deferral log is kept by the facility, and users interested in this information should contact Dr. Rita Hannah. Users who have been deferred should resubmit a time request for the following month. NMRFAM cannot make assumptions about a user’s continued need to access a particular instrument across time.

Routine spectroscopy of submitted samples is available twice weekly on a first-come-first-serve basis on the DMX 400. See the schedule via the Sesame module Sundial. Application forms may be obtained from Dr. Rita Hannah or downloaded from the NMRFAM web site. An abstract describing the proposed project must be submitted with the time request (or already be on file at NMRFAM).

(2) Off-line workstations.
Outside users should contact Dr. Milo Westler (milo@nmrfam.wisc.edu) to reserve time on the workstations.

Remote data collection:
Users can arrange to submit samples (or bring them) in for remote data collection. Information on setting this up is on the website.

User fees:
Fees will be waived if problems develop as the result of equipment failure, but not for problems resulting from sample quality, quantity, or outside operator error.

$50/hr

If an industrial user plans on publishing the data collected at NMRFAM within one year, then the academic rate is charged.

(1) NMR data collection (minimum charges are for 0.5 hr)

(2) Surcharge for staff assistance with data acquisition or analysis:
$50 each hour (minimum 1 hr). Long unattended runs are charged for spectrometer time only.

(3) Training of users:
$50 per hr (minimum 1 hr). Before independent use of any of the facility instruments, all users must be trained. Facility staff will oversee this training, and solo use on a particular class of experiment will not be permitted until the staff is satisfied that a minimum competency level is reached. New users receive up to 8 hours of free training.

(4) Data stations:
No charges are levied at present.

(5) Routine spectroscopy of submitted samples:
$50/hour (minimum 0.5 hr).

Sources of funding and suggested acknowledgment in publications:

Equipment in the facility has been purchased with funds provided internally by the University of Wisconsin-Madison Graduate School, School of Agricultural and Life Sciences, and Biochemistry Department and externally from the National Institutes of Health, the National Science Foundation, and the U.S. Department of Agriculture. Day-to-day operation of the facility is supported by a grant from the NIH Biomedical Research Technology Program, National Center for Research Resources, user fees, and funds from the University of Wisconsin-Madison.

Publications resulting from use of NMRFAM should acknowledge the facility. The following wording is suggested:

“This study made use of the National Magnetic Resonance Facility at Madison, which is supported by National Institutes of Health grants P41RR02301 (Biomedical Research Technology Program, National Center for Research Resources) and P41GM66326 (National Institute of General Medical Sciences). Equipment in the facility was purchased with funds from the University of Wisconsin, the National Institutes of Health (P41GM66326, P41RR02301, RR02781, RR08438) , the National Science Foundation (DMB-8415048, BIR-9214394), and the U.S. Department of Agriculture.”

All Publications that contain data collected at NMRFAM must be submitted to PubMed Central according to the NIH Public Access Policy. For more information about the NIH policy and PubMed Central Submission instructions, please go to http://publicaccess.nih.gov/.

As part of its yearly reporting obligation, NMRFAM will contact users to obtain references to publications that have made use of the facility. Users also will be asked to provide a brief summary of their work for the NMRFAM Annual Report.

Suggestions or complaints:
Kindly address these to the Director of NMRFAM or to the Chair of the National Advisory Committee:

Kevin H. Gardner, Ph.D.
Professor of Biochemistry
Virginia Lazenby O’Hara Chair in Biochemistry
Chair, Molecular Biophysics Graduate Program
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel: (214) 645-6365
Fax: (214) 645-6353
e-mail: Kevin.Gardner@utsouthwestern.edu