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Protein Crystallography Data Collection Service at BL38B1

The Japan Synchrotron Radiation Research Institute (JASRI) has been providing the protein crystallography data collection service at BL38B1 since 2009B. We hope that our service will contribute to your R&D efforts by offering the experimental results with the world's highest accuracy in X-ray structure analyses of biopolymers, which is indispensable for research and development of new drugs, unknown chemicals and environmental agents, etc. Interested applicants are encouraged to apply.

[Contents]

1. Service Overview
2. Beamline
3. Sample Preparation
4. Fees
5. Application Method
6. Review Criteria
7. Post-Implementation Processes
8. Consultation/Contact



1. Service Overview

The staff of the JASRI will perform measurements on protein crystal diffraction patterns using the SPring-8 beamline, BL38B1, on behalf of users. Therefore, users can choose whether to come to SPring-8 and be present during the measurements or to simply send or hand-deliver their samples to the SPring-8.

The service is intended to provide convenience for users who are not familiar with protein crystal structure analysis and experienced users wishing to obtain measurement data in a timely manner.

Application for the service is considered a proprietary proposal and is subject to proprietary beamtime fee and user fee applicable to proprietary Time-Designated Proposals. (See 4. Fees.)

We keep confidential any confidential information received or acquired during the course of the service; and you have no obligation to disclose your application details or research results. In addition, you/your organization are the sole and exclusive owner of the entire right, title and interest in and to the research results obtained through the use of the service and any resulting patent or other form of intellectual property.

We accept applications on an as-needed basis. For inquiries about the dates available for the service or for information about the processes and procedures, please contact the JASRI staff (see 8.1 Consultation/Inquiries about the Service/Sample Shipment).

2. Beamline

BL38B1  Structural Biology III
For details about the facility, please visit the SPring-8 Protein Crystal Analysis Division website.

3. Sample Preparation

3.1 Preparation
Samples must be prepared in advance in a special cryo-pin for measurements using SPACE (SPring-8 Precise Automatic Cryo-sample Exchanger). For instructions on how to prepare samples, click here.

To ship your samples from outside Japan, you need to be aware of regulations covering international shipping of chemicals. Please note that you need to go through all required steps (e.g. paperwork, customs procedures, etc.) required for entry of your samples to Japan at your own risk and expense: we cannot assist you with this.

If you have any questions or encounter any problems, contact the JASRI staff (see 8.1 Consultation/Inquiries about the Service/Sample Shipment).

3.2 Unacceptable Samples
The safety review is conducted based on the safety criteria of the JASRI. We only accept biomacromolecular crystals and the following chemicals classified as Level 4 by the JASRI (i.e. substances requiring the approval of the competent authority) are not accepted. If you wish to use heavy atom derivatives (incl. heavy metals), please contact the JASRI staff (see 8.1 Consultation/Inquiries about the Service/Sample Shipment).
- Specific substances regulated by the "Law on the Prohibition of Chemical Weapons and the Regulation of Specific Chemicals"
- Narcotic and psychotropic drugs regulated by the "Narcotics and Psychotropics Control Law"
- Stimulant drugs and ingredients of stimulant drugs regulated by the "Stimulant Drug Control Law"
- Hemp and hemp products regulated by the "Cannabis Control Law"
- Opium, poppy or poppy straw regulated by the "Opium Law"
- Scheduled drugs by the "Pharmaceutical Affairs Law"
- Specified poisonous substances regulated by the "Poisonous and Deleterious Substances Control Law"
- Substances for which manufacturing is prohibited under the "Industrial Safety and Health Law"

4. Fees

Users are required to pay the following fees:

a) Beamtime Fee
Based on the measurement method and the number of samples/data sets, beamtime is allocated in increments of two hours. Please discuss beamtime calculations with the JASRI staff (see 8.1 Consultation/Inquiries about the Service/Sample Shipment) beforehand and agree on the required beamtime, for which proprietary beamtime fee for time-designated use is charged.

    Beamtime Fee: 180,000 yen/2 hours incl. tax

b) User Fees
Users are required to pay the fees to cover the costs of beamline maintenance/operation and consumables actually used (user fees). The user fees are composed of a fixed fee charged for wear and tear on the facility and a variable fee charged for liquid He, He gas, and the stockroom reagents, parts, and stationery.

    Fixed Fee: 2,640 yen/2 hours incl. tax
    Variable Fee: calculated based on the amount actually used for measurements

An invoice will be sent after the event.

5. Application Method

5.1 Submission of Application Form
To apply for the service, please submit an "Application for Measurement Service (Form A)" and a "Conditions for Crystal Evaluation (Form A_1)" to the Protein Crystal Analysis Division at mail-in@spring8.or.jp as email attachments. (You will be requested to protect your files with a password and give the password to the staff on the phone.) In the subject line of the email, type: Application for Protein Crystallography Data Collection Service. Applications may be submitted at any time. If you have any questions, please contact the JASRI staff (see 8.1 Consultation/Inquiries about the Service/Sample Shipment

5.2 Preliminary Arrangements
Upon receipt of the application, the JASRI staff will contact and discuss service details with you. (You can choose whether to come to SPring-8 for discussions or not.) After the discussions, the staff will send you the "Service Confirmation Form (Form B)" for you to refer to when you submit a proposal online (See 5.3 Online Proposal Submission).

5.3 Online Proposal Submission
Upon receipt of the "Service Confirmation Form (Form B)," your application needs to be submitted as a research proposal from the User Information website (UI site) online, not by post, courier, fax, email or by hand-deliver.

User Information Website (UI site) > Log in to My Page > Proposal/Use Plan Submission under Application/Reporting > New > Proprietary Research + Measurement Service Proposal

First, log in to the system with your user card ID number and password. If you have not obtained your user card ID number, please complete user registration first to create your user account.

  Submission Deadline: 10:00 a.m., 10 business days before the scheduled date of data collection

Upon successful online proposal submission, you will receive a confirmation email with the proposal application number attached to it. Please provide the application number and all other information on a "SPring-8 Measurement Service Agreement," have the person responsible for the payment of fees sign the Agreement, and then send it by post to the Users Office (See. 8.2 Inquiries about Online Proposal Submission/Document Submission).

Note that only the spokesperson can submit the proposal: if a collaborator needs to submit the proposal in place of the spokesperson, he or she must log in to the spokesperson's account. In this case, the spokesperson is responsible for managing his or her account information.

5.4 Document Submission
After the online proposal submission, the Users Office will request you to submit the following documents:
a. Application Form for SPring-8 Facilities

- If you wish to attend the measurement sessions:
Contact and consult with the JASRI staff in advance and submit the "Application Form for SPring-8 Facilities" online from the UI site (My Page > Application/Reporting > Before Arrival > Application for SP8 Facilities) at least 10 days before visiting SPring-8. On the form, please provide the expected receive/return dates of user card and dosimeter and the expected Guest House check-in/check-out dates.

- If you are not going to attend the measurement sessions:
Check the box for "Off the list," and provide the scheduled date/time of measurements specified on Form B.

b. Radiation Worker Registration Form (Form 5-1)
If you wish to attend the measurement sessions, please submit a Form 5-1 at least 10 days prior to your visit. For further details, please contact the JASRI staff at mail-in@spring8.or.jp.

c. List of Samples, Reagents, etc.
After submitting the " Application Form for SPring-8 Facilities", please also submit a "List of Samples, Reagents, etc." online from the UI site. Note that the link to this form is not displayed until after the "Application Form for SPring-8 Facilities" has been submitted.

5.5 Sample Shipment
Please make sure that your samples are properly prepared and have been made suitable for measurements in advance (See. 3.1 Preparation). If you are uncertain about how to prepare your samples, please consult the JASRI staff at: mail-in@spring8.or.jp. If you need to ship your samples to us, send them to the Users Office (See. 8.1 Consultation/Inquiries about the Service/Sample Shipment). Please note that shipments can be received only during normal business hours (9:00 am – 5:00 pm) on weekdays.

6. Review Criteria

Only safety of experiment are reviewed. Technical feasibility, sociality and ethicality of experiment are not reviewed (already recognized through the consultation process with JASRI staffs). Scientific and technological relevance and necessity of SPring-8 as a research tool are not reviewed.
<Important Notice>
If your samples are poisonous or hazardous materials regulated and not permitted to send by the law, it may be possible that you must carry your samples into/out the SPring-8 by yourself.

7. Post-Implementation Processes

The measurement data and the measurement report will be sent to you. The data will be delivered in electronic format such as CD-ROM that you provide with us or via the Internet. Please note that the analysis of the measurement data is not part of our service. For information about analysis software and/or analytical methods, please contact the JASRI staff (See. 8.1 Consultation/Inquiries about the Service/Sample Shipment).

After checking the data and report, please submit the "Beamtime Report" online from the UI site.

Your samples will be returned to you after the measurement sessions. For users who did not attend the sessions, the JASRI staff will send back the samples at users' cost. In this case, the users are required to return the "Sample Receipt Form (Form C)" to JASRI upon receipt of the samples.

Following the measurement report, data and samples, the invoice will be sent to you. Please make sure that your organization makes payment of the fees (See 4. Fees).

The results obtained through the service (measurement data) belong to your organization.

Please give us feedback on the measurement service. Your views are very important to us and we welcome your comments and suggestions that will help us improve the service we provide and make it more attractive to our users.

8. Consultation/Contact

8.1 Consultation/Inquiries about the Service/Sample Shipment
To apply for this service, please first contact:
  Seiki Baba
  Protein Crystal Analysis Division
  Japan Synchrotron Radiation Research Institute (JASRI)
  1-1-1 Kouto, Sayo-cho, Sayo-gun
  Hyogo 679-5198 JAPAN
  Tel: +81-(0) 791-58-0833
  email: mail-in@spring8.or.jp

8.2 Inquiries about Online Proposal Submission/Document Submission
  SPring-8 Users Office, User Administration Division
  Japan Synchrotron Radiation Research Institute (JASRI)
  1-1-1 Kouto, Sayo-cho, Sayo-gun
  Hyogo 679-5198 JAPAN
  Tel: +81-(0) 791-58-0961
  email: sp8jasri@spring8.or.jp

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