SPring-8 PX-BL automatic data collection

2023/4/12• Easy to use– Procedure is basically same as that of on-site manual data collection.
Registration of radiation worker is not requested.
– Send samples packed in UniPuck.
– Data collection and data process are conducted automatically.
• Automatic data collection using ZOO system @ BL45XU / BL32XU(https://doi.org/10.1107/S2059798318017795)• Automatic data process using KAMO system (Your licensing for XDS is needed)(https://doi.org/10.1107/S2059798318004576)– Data is sent back together with the sample.

• High accuracy, Fast, Low cost

– Data collection is conducted by using brilliant microbeam, a fastsample changer and a pixel array detector.
– Typical data collection time is 4 ー 7 minute / loop (Note that it
depends on sample and measurement method).
– In the case of proprietary use, the cost per one sample is about
10,000 JPY. (The real cost is charged by time basis.)
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PX-BL automatic measurement operation rules【Terms of use】
・You must agree to the agreement form.

【Radiation registration】
・It is not necessary if you can leave your samples to the staff. See page 7.
・If you cannot do so, radiation registration and its education are required.
【Estimation of measurement time】
・Refer to the attached table. See pages 8 and 9.
【Measurement schedule】
・Please fill in the experimental information on the automatic measurement sample
sheet, and send it by the deadline. We will discuss the measurement conditions basedon your request.
・The measurement schedule will be assigned based on the previous request. However,
we will combine two or more measurement tasks from different proposals forefficiency. Please note that it is not possible to handle exact scheduling.
・There are restrictions in schedule for automatic data collection by “Additionalrecruitment beam time” and “Proprietary time-designated proposals”, so please contact
us in advance.
【Sample sending】
・Please send by 17:00 on the deadline date.
・If arrival is delayed, it will be treated as a cancellation.
・Samples are to be sent to the USERS OFFICE.
The detailed information: https://user.spring8.or.jp/?p=36857&lang=en
Contact for shipping:sp8jasri@spring8.or.jp

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Procedure for PX-BL automatic data collection (General proposal without visitation)
Procedure[Beamtime (BT) survey request]

User

・We will perform the survey five time per year in principle (Operation period A： 2 times, B period 3 times)
・Minimum allocation unit for beamtime slot: BL45XU, BL32XU : 0.25 shift (2 hours)

SPring-8
Beamtime survey (e-mail)[Reply to the survey request]

・Please estimate required beamtime shift by referring to the pages 8-9 in this document.

<Proprietary use>

・Please send information about the selected beamline, the number of shifts, the preferred date and request of automatic
data collection via e-mail to “pxbl@spring8.or.jp”.

<Non-proprietary use>

・Please upload “Crystal specification sheet” and “Beamtime survey sheet” (check automatic data collection) on the Web site(http://bioxtal.spring8.or.jp/survey/index2.html).

Reply the survey(non-proprietary use: Web,proprietary use: e-mail)

SPring-8 Program Review
Committee, L1
Subcommittee
pxbl@spring8.or.jp[Decision and announcement of your beamtime]

・We will announce decision for your beamtime (number of shifts, beamline, and schedule). Data collection would be
conducted considering the assigned BT. However, its date and time could be different from the assigned BT.

[Procedure for use] 10 days before BT

Announcement of BT

・Please submit “Application for SPring-8 facilities” and “List of Samples, Reagents, etc. ” from your “My Page” of SPring-8
UI Site (http://user.spring8.or.jp/). See page 7.
・Please contact us if your experiments contain genetic recombination experiment such as protein production by bacurovirus.

Application form for SPring-8 facilities(form 10), List of Samples, Reagents,etc (form 9)

Users Office[Determination of measurement condition] 2 days before BT (at BL45XU, see page 4)

Sample sheet (e-mail)

Automated measurement personnel
mail-in@spring8.or.jp

・Please fill and send the “Sample sheet for automatic data collection” at least two days before the beamtime. See page 6 tofind its URL. This form will be frequently updated, then please use newest version of it by checking its URL.
・Please refer to "How to entry automatic measurement sample sheet" to fill in the sample sheet.
・We will arrange the measurement condition based on your sample sheet and will send the final version of the sample sheet
to you for confirmation.

Determination of measurement condition (e-mail)Sample sheet filled with themeasurement condition (e-mail)[Sending the agreement form] One day before BT

・ Please submit “SPring-8 PX-BL Automatic Data Collection Agreement form” from your “My Page” of SPring-8 UI Site
(http://user.spring8.or.jp/)
・The agreement form is only required in the first beamtime assignment of each proposal. See page 10.

[Shipping samples hard disk drive] One day before BT (at BL45XU, see page 4)・Please ship samples, a HDD for data storage (and invoice for return) to us. The items should be delivered to SPring-8 by
the day before BT. If arrival is delayed, we could not conduct experiment.
The detailed information: https://user.spring8.or.jp/?p=36857&lang=en[Conduct automatic data collection][Send back sample and data]

・Please refer “Data from automatic data collection at SPring-8”.

Agreement Form (Web)Users Office

Shipment of Sample, HDD

Users Office
Automatic data collection
Send back sample, HDD3The operation of BL45XU (Automatic measurement ) was changed.
 Divide the week's allocation into two periods(three days,four days).
 To support long-time automatic measurement by the Uni-Puck automaticexchange system.
（Test operation in 2020A, in service from 2021A）
 Operation covered for problems with interruptions in measurement.
 Extension of measurement time can be selected.
(However, it is only available when there is open beamtime.) In the Wednesday-Friday allocation, the dry shippers must arrive Tuesday.
（Deadline for sample sheets is Monday）
 In the Saturday-Tuesday allocation, the dry shippers must arrive Friday.
（Deadline for sample sheets is Thursday）
 Measure in the order in which the samples arrive.

Last operation

Operation from October 2020

Samples arrived << Tuesday

Samples arrived <<Samples arrived <<Green ：proprietary proposal

Pink：unproprietary proposal

4Procedure for PX-BL automatic data collection (Proprietary Time-Designated Proposals without visitation)

Procedure[Consult a beamline staff]

・Coordinate with beamline staff (schedule and number of shift for automatic measurement)[Submit proposal]

・ Submit proposal from the web site of Users Office (https://user.spring8.or.jp/?lang=en)
・ Please check the detailed information about Proprietary Time-Designated Proposals(https://user.spring8.or.jp/?p=34156&lang=en)

UserSPring-8

Consult about date, number ofshifts (by e-mail)Beamline staff

Submit proposal（on line）

Users Office[Decision and announcement of your beamtime]

Announcement of BT

・We will announce decision for your beamtime (number of shifts, beamline, and schedule). Data collection would beconducted considering the assigned BT. However, its date and time could be different from the assigned BT.

[Procedure for use] 10 days before BT・Please submit “Application for SPring-8 facilities” and “List of Samples, Reagents, etc. ” from your “My Page” ofSPring-8 UI Site (http://user.spring8.or.jp/). See page 7.
・Please contact us if your experiments contain genetic recombination experiment such as protein production bybacurovirus.

[Determination of measurement condition] 2 days before BT

・Please fill and send the “Sample sheet for automatic data collection” at least two days before the beamtime. See page
6 to find its URL. This form will be frequently updated, then please use newest version of it by checking its URL.
・Please refer to "How to entry automatic measurement sample sheet" to fill in the sample sheet.
・We will arrange the measurement condition based on your sample sheet and will send the final version of the sample
sheet to you for confirmation.

[Sending the agreement form] One day before BT

・ Please submit “SPring-8 PX-BL Automatic Data Collection Agreement form” from your “My Page” of SPring-8 UI Site
(http://user.spring8.or.jp/)
・The agreement form is only required in the first beamtime assignment of each proposal. See page 10.

[Shipping samples hard disk drive] One day before BT

・Please ship samples, a HDD for data storage (and invoice for return) to us. The items should be delivered to SPring-8
by the day before BT. If arrival is delayed, we could not conduct experiment.
The detailed information: https://user.spring8.or.jp/?p=36857&lang=en[Conduct automatic data collection][Send back sample and data]

・Please refer “Data from automatic data collection at SPring-8”.

Application form for SPring-8 facilities(form 10), List of Samples, Reagents,etc (form 9)

Users OfficeSample sheet (e-mail)

Automated measurement personnel
mail-in@spring8.or.jp

Determination of measurement condition (e-mail)Sample sheet filled with themeasurement condition (e-mail)Agreement Form (e-mail)Users Office

Shipment of Sample, HDD

Users Office

Automatic data collection
Send back sample, HDD

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Necessary document and destination for submission【Beamtime survey】<proprietary use>
・Send request via e-mail<non-proprietary use>
・Crystal specification sheet
・BT survey sheet
・Web site for the upload:e-mail address: pxbl＠spring8.or.jp
http://bioxtal.spring8.or.jp/index_files/Crystal_Spec_Sheet.pdf
http://bioxtal.spring8.or.jp/index_files/Beamtime_Survey_Sheet_en.pdf
http://bioxtal.spring8.or.jp/survey/index2.html【Before beamtime】
・Application form for SPring-8 facilities (form 10) https://user.spring8.or.jp/?p=26855&lang=en
・List of Samples, Reagents, etc (form 9)
https://user.spring8.or.jp/?p=26840&lang=en
Procedure for radiation worker is requested, if you cannot include the anonymous beamline staff (ID: 0052000) in the Application Form.
・Registration of a radiation worker
https://user.spring8.or.jp/?p=26820&lang=en
・Radiation safety training (e-learning)https://user2.spring8.or.jp/?page_id=722&lang=en【Agreement form】
・Agreement Form for automatic data collection (form F01-PA)
https://user.spring8.or.jp/?p=29468&lang=en
Refer to page 10 for the information on Agreement form.
【Sample, Sample information】
・Samples are to be sent to the USERS OFFICE
・Contact for shipping

https://user.spring8.or.jp/?p=36857&lang=en
e-mail address: sp8jasri@spring8.or.jp

・Sample sheet for automatic data collection
http://bioxtal.spring8.or.jp/en/users/Auto/ZOOPREP_YYMMDD_NAME_BLNAME.xlsx
・How to entry automatic measurement
http://bioxtal.spring8.or.jp/en/users/Auto/PXBL_Auto_sample_sheet_manual_en.pdf
sample sheet
・Data from automatic data collection at SPring-8 http://bioxtal.spring8.or.jp/en/users/Auto/Data_from_automatic_data_collection_
at_SPring-8_en.pdf【Inquiry about automatic measurement】
・Automated measurement personnel

e-mail address: mail-in@spring8.or.jp

6Online Submission of Application Form for SPring-8
Facilities for PX-BL automatic data collection
1.

From “Change Project Team Member”, please add Beamline Staff (ID:0052000).

2.

From “Application Form for SPring-8 Facilities”, select “Absence" from the pull-downmenu except Beamline Staff (ID:0052000).
Please enter your beamtime in the “Receive” and “Return” boxes, and put checks the“NO NEED FOR GUEST HOUSE RESERVATION” check box. Moreover, Please enter ”Novisit for automatic data collection” in the message column.

3.

Absence

7Calculation of measurement time
Total measurement time = Setup time ＋ Measurement time per sample pin x Number of pins
・Please apply for beam time every 2 hours for BL45XU and BL32XU.
・Setup time: 15 minutes (Time required for beam adjustment and sample setup.)
・Measurement time per sample pin : Refer to the table below.

Experimental schemes

Wedge size (/crystal)Time for a loop

5-10 deg.

~ 10 min( 30 crystals, 500 x 500 um loop)“Helical”
single or a few crystals

90-360 deg.

~ 7 min (helical)“Single”
single or a few crystals

90-360 deg.

~ 4 min (single)“Small wedge”
10–300 crystals

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Average time for automatic measurement at BL45XU

Measurement time per sample pin (min.)

9Agreement form for theautomatic data collection• Downloads the form from here.
https://user.spring8.or.jp/?p=2946
8&lang=en• Please fill in the agreement formand submit it from your “My Page”
of SPring-8 UI Site.
http://user.spring8.or.jp/⇒• Deadline:
By the day before Beamtime.
• Once the form is submitted, it isvalid while the proposal is valid.
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Example of results using PX-BL automatic measurement (proprietary use)
Type
Compound screening
Crystal screening
Experiment condition @ Spring-8 BL45XU
128 pins (8 pucks)
Number of Sample 78 pins (7 pucks)
8 hr 13 minExperimental time 6 hr 49 min
Average Experiment
5 min 15 sectime par samples

Beam size
Flux
Typical crystal size

3min 51 sec
20μm x 20μm
20μm x 20μm
1.73 x 1013 photons / sec 1.73 x 1013 photons / sec
200μm in length

Automatic data collection by ZOO
Raster Scan

78 pins

Data Collect77 pins

Typical scan area :250 x 200 or
400 x 300μm,
Exposure = 0.02 sec / fr,
10% Flux
Mode = Helical,
ΔΦ = 0.1deg / fr,
TotalΦ = 360deg,
Total dose = 10MGy,
Exposure = 0.02 sec / fr,
100% Flux,
Camera dist = 250mm

50128 pins

121 pins

Automatic data processing by KAMO (XDS)
Total : 77 sets
Processed-150μm

Typical scan area :250 x 200 or 300 x 250 or
550 x 450μm,
Exposure = 0.02 sec / fr,
5% Flux
Mode = Single (102pins) or
Helical (9pins),
ΔΦ = 0.2deg or 0.5deg / fr,
TotalΦ = 360deg,
Total dose = 10MGy,
Exposure = 0.02 sec / fr,
1.2 or 2.9% Flux,
Camera dist = 180 - 600mm

Indexing failed : 1set,Indexing failed : 5set,
Complete(comp. > 90%) : Total : 121 sets Complete(comp. > 94%) :76 sets
116 sets

Beyond 2.5Å 36 datasets
3.0 - 2.5Å 35 datasets
5 datasets
Low resolution sets
(12.4 - 3.8Å)

Beyond 2.0Å 33 datasets
3.0 - 2.0Å 25 datasets
58 datasets
Low resolution sets
(9.17 - 3.03Å)

Small wedge (multi mode)
73 pins (6 pucks)
11 hr 19 min
8min 23 sec
10μm x 10μm
9.75 x 1012 photons / sec

5-20μm (Membrane protein-LCP)
Typical scan area :600 x 550 or800 x 700 or
73 pins 1000 x 800 μm,
Exposure = 0.02 sec / fr,
35% Flux
Mode = Multi,ΔΦ = 0.1deg / fr,TotalΦ = 10deg,Total dose = 10MGy,
64 pins Exposure = 0.02 sec / fr,
10.7 % Flux,
Camera dist = 380mm

Total : pins, data sets, [outer shell] Resolution,
940 sets Completeness, CC1/2 , I / Sigma
Sample A: 30, 287, 1.92Å,99.6%, 57.2, 1.56
Sample B: 23, 446, 2.04Å,99.8%, 83.2, 1.42
Sample C: 9, 190, 4.78Å,99.8%, 64.0, 1.94
2, 17, Processing was not possible
Sample D: due to a small number of data sets11Results of PX-BL automated measurementin 2019A/B,2020A
Proposal Type

Non-proprietary
Proprietary
Total

Proposal Type

Non-proprietary
Proprietary
Total

Number of unique
Total beam timeusers(times)(groups)

58
2280

182
200
380

Average time per Minimum time perbeam time(hours) beam time(hours)

10.0
7.9
8.9

222Total beam time(hours)

1820
1578
3398
Maximum time
per beamtime(hours)

36
2236

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Revision history
2019.09.11 Added information on how to write online application.
2019.09.12 Added page number.
2019.09.18 Added “PX-BL automatic measurement operation rules” and “Calculation of measurement time “ and“Automatic measurement time results at BL45XU”. Changed the sample destination.
2019.09.20 Add information on sample shipping and agreement form.
2020.02.19 Changed minimum beam time of BL32XU.
2020.05.28 Added contact information, examples of automatic measurement results.
2020.09.17 Change in the deadline for sample sheets and sample arrival at BL45XU.
2021.01.05 Abolition of sample receipt form, Link changes due to UI site changes.
2021.03.09 Changing the destination of a shipment.
2021.03.31 Added a hyperlink to the document on the “Procedure for PX-BL automatic data collection” page.
2021.09.09 Changes in description due to electronic file submission of automatic measurement agreement form.
2022.11.22 Corresponded to GUI changes for Submission of Application Form.
2023.04.12 Changes to how to submit “Agreement form for the automatic data collection”.

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