1. Microfocusing X-ray Protein Crystallography Beamline
Zengqiang Gao
beamline
17/12/2019

2. Table of Contents Scope and objective Outcome of the review 2018
Status of work progress
Summary of authorized changes
Manpower
Risks and mitigation
Schedule and major upcoming milestones

3. Scope and objective
Determine the crystal structures of vital proteins in life sciences
S. F., Yang et al,
Nature, 560,
Membrane proteins (GPCR et al)
Huge complex (ribosome et al)
Ferbitz, L. et al,
Nature, 431,
Other proteins
Serving as the platform for drug discovery
Hubbard, R.E.,
J. Synchrotron Rad. 15, 227–230
High throughput/automatic

4. Table of Contents Scope and objective Outcome of the review 2018
Status of work progress
Summary of authorized changes
Manpower
Risks and mitigation
Schedule and major upcoming milestones

5. Outcome of the review 2018 Type Description Response Comment
Protein crystallography is a continuously developing field. Look carefully around the world status and choose best-possible endstation system in the latter half of the project. In contrast, the beamline is more or less standard which can be finalized in an earlier stage
All the components of MX beamline will be installed at the end of 2023, and the commissioning with x-ray beam will be start at the beginning of 2024
The heat-load level is manageable with cryogenic silicon monochromator without the white beam mirror. Less numbers of optical components can make the beam stability better and make the life easier. If it is not enough, consider a diamond window instead of the WBM
White beam mirror has been removed
The beamline optics goal may be reached by the combination of only the HDCM and CRLs. Since the CRL is a chromatic component, design a mechanism to fix the focal spot. The mechanism may also be used for changing the beam size by defocusing.​
We use HDCM and K-B mirror to get the 1µm spot and keep higher flux at the same time. CRL is used to get the larger spot (30µm)

6. Outcome of the review 2018 Type Description Response Comment
Most likely, the combination of cryo-sample with serial crystallography is not necessary. Room temperature measurement does not necessarily couple with the low range of degree especially for serial crystallography
Room temperature/in situ with SSX will be the dominating experimental method.
From the users’ point of view, it is comfortable to use the same software (preferably the software pipeline) between SSRF and HEPS. The ideal situation may be to set up a consortium to develop the software pipeline among SSRF, HEPS, TPS, PLS and SPring-8​
The data processing pipeline will be same as, even identical with, that of SSRF. The data collection software (GUI) maybe different from that of SSRF.
Serial crystallography for LCP based membrane proteins may not be fit with ‘jet’-scheme. Consider a new method for the LCP based crystallography​
Fixed-target system or High-viscosity extrusion (HVE) injector will be used for LCP based proteins.

7. Table of Contents Scope and objective Outcome of the review 2018
Status of work progress
Summary of authorized changes
Manpower
Risks and mitigation
Schedule and major upcoming milestones

8. Status of work progress — optical layout
Spot size(FWHM, H*V)
41.2µm*17.6µm
Energy resolution:
1.6/12400=1.3×10-4
Spot size(FWHM, H*V)
0.7µm*0.8µm
Energy range: 5-18keV
Energy
Spot size(FWHM, µm): 1-30 (discrete)
Flux :
31.5m m 45m m 50m m 52.9m m
undulator
Shielding wall
White slit
HDCM
CRL
VFM HFM sample
Mono slit
Design principle: as less optics as possible
1µm spot: HDCM + KB mirror
Larger spot: HDCM + KB mirror + CRL
Spot divergence(FWHM, H*V)
1.2mrad*0.8mrad
Spot divergence(FWHM, H*V)
11.6µrad*12.6µrad

9. Status of work progress — Light source
Storage ring
undulator
energy
6 GeV
Type
IAU
Phase error（RMS）
 4°
current
200 mA
Brightness
6.51021
phs/s·mrad2·mm2·0.1%BW
emittance
60pm.rad
Total length 5m
Periodic length
32.7mm x
10.12m
flux
2.11015
phs/s·0.1%BW y
9.64m
1st order energy
keV
Total power
14.3kW
Energy spread
1.06E-3
K value
Center power density
336kW/mrad2
x/x
18.5m/1.83rad
magnetic field
0.8T
Beam
41.1μm (H) × 17.4μm (V)
y/y
6.2m/
0.64rad
Min gap
11mm
Beam
13.3μrad (H) × 12.8μrad (V)
1st
3rd
5th
Flux curve
Brill. curve
Power density
distribution

10. Status of work progress — HDCM
Parameter (unit)
Value
Distance to light source (m) 45
Accept divergence (μrad)
22×22
Crystal surface
Si<111>
Energy (keV)
5~18
Bragg angle ()
6.31~23.29
Designed bragg angle ()
-4~30
type
Fixed offset
Reflection direction
horizontal
Offset (horizontal, mm) 20
Offset deviation(µm)
≤10
Max slope error due to heat (RMS, μrad)
0.32
Cooling method
LN2
Base material
granite
∆E/E = 1.6/12400=1.29×10-4 (Xrt)
∆E/E = 1.25×10-4 (XOP)
Max temperature:
Energy resolution: ~1.3×10-4
Shape/slope error deformation (meridian)：
0.06nm/0.32rad
Shape/slope error deformation (sagittal)：
0.018nm/0.35rad
Next plan: replace the DCM with
channel-cut monochromator (CCM),
theoretical calculation is going on.

11. Status of work progress — KB mirror
parameter（unit）
VFM
HFM
Object distance（m）
52.56
52.9
Accept divergence (μrad)
17×17
type
Fixed shape
Image distance（m）
0.8
0.46
Energy range（keV）
5～18
Mirror size(L×W×H，mm3)
300×50×50
Sagittal slope error（rad） 1
Meridian slope error（rad）
0.2
roughness（Å） 3
Surface direction
Horizontal
vertical
Meridian type
Cylinderial
Reflection angle（mrad） 3
coating Rh
KB mirror is also used for high order
harmonic rejection:
Si (the mirror surface) for 1st order
Rh for 3rd and 5th order
Spot size: 0.68m(H)×0.76m(V);
Flux: 7.11×1013ph/s
Tracing result with DCM shape
error by heat and KB slope error

12. Status of work progress — CRL
N of lens
Spot size
(H×V, m)
Flux
(ph/s) 1
3.2×9.0
6.78×1013 2
7.0×18.4
6.58×1013 3
10.0×29.0
6.41×1013 4
14.8×32.4
6.22×1013 5
22.0×42.8
6.05 ×1013 6
25×48.2
5.89 ×1013
Parameter (unit)
Value
Object instance (m) 50
Accept divergence (μrad)
17×17
Radius at apex (m)
200
Geometry radius (m)
900
Material Be
Number of lens 6
Two methods to change spot size：
Change the number of CRL lens
Use all lenses, change the size by pinhole
R=200，N=1
R=200，N=3
R=200，N=6
The beam distribution becomes more uniform with the number of lens increase

13. Slope error and stability analysis
Angular stability
Position stability
Depends on the Magnification factor (p/q)
Optical elements parameters:
LDCM=45m, LVFM=52.56m, LHFM=52.9m, MVFM=65.7, MHFM=115
Sdm=2×2.355×Δθ×L/M
Sds=2×2.355×Δθ×sinθ𝑖×𝐿/𝑀
Optical element
Slope error (M/S)
HDCM
0.3μrad/1μrad
VFM
0.2μrad/1μrad
HFM
name
H/meridian
Deviation at Sample
V/sagittal
Light source
41.1μm
0.036μm
17.4μm
0.026μm
HDCM angle deviation
0.1μrad
0.18μm
0.08μm
VFM angle deviation
0.57μm
3μrad
0.38μm
VFM position deviation -
1μm
0.02μm
HFM angle deviation
0.22μm
0.03μm
HFM position deviation
0.01μm
beam size
Without deviation
0.93μm
0.95μm
With deviation
0.97μm
1.03μm
Deviation ratio (rms)
4.8%
8.0%
Angle deviation
HDCM
50nrad
80nrad
100nrad
150nrad
VFM
110nrad
HFM
Deviation ratio (H/V)
1.3%/
2.2%
3.1%/
5.2%
4.8%/
8.0%
10.2%/
9.9%

14. Status of work progress — Experimental methods
Conventional
crystallography
Serial
Common (low temperature，loop)
In-situ (room temperature，plate)
First stage
Fixed-target sample delivery
Key area of development
Jet-based sample delivery
Local access
Remote access

15. Status of work progress — endstation hardware
detector：
Frame rate：>100Hz Z X Y
Yaw
Roll
Pitch
X-ray out
X-ray in
Detector
diffractometer
KB Mirror
Robot
Eiger
Detector developed by IHEP
diffractometer: MD3-up Sphere of confusion (SOC): 0.1μm
Layout of experimental endstation
(by Dr. Hao, Liang)
Robot: ISARA
Time for sample change: ≤10s
Success ratio: ≥99.99%
Generals hardwares will be available through
the commercial products.

16. Hardware-Sample delivery system
Jet-based
S. Sui et al., Struct Dynam-Us 4, 2017,
C.Y. Huang et al, ActaD, 2015, 1238
P. Roedig et al., nature methods, 2017, 14, 805
Fixed target
G.R. Guo et al, IUCrJ (2018). 5, 238–246
In-situ, fewer crystals
Only be used as a holder
In-situ, many crystals
An employee will be hired to
develop this kind of instrument
in next year!
Fixed target system (Chip-based) will be the first choice for SSX experiment in HEPS (at least in the first stage).

17. Status of work progress — software
Integrated new hardware control into the original MXCuBE GUI successfully!
The data collection software (GUI) has been identified to be MXCuBE

18. Status of work progress — software
Data processing software
individual
Data process: HKL2000/3000, Xia2(ccp4); XDS; Fast_dp (Diamond); Go.com (SLS);
Phase determination: Phenix.autosol; Phaser; MrBUMP: AutoSHARP
Serial data process: XDS/CrystalFEL/facility unique
pipeline
K. Yamashita et al, Acta Cryst. D,2018, 74, 441–449
F. Yu et al J. Appl. Cryst. (2019). 52, 472–47
Standard data: using the current software (integrate it into pipeline)
SSX data: develop our own software based on current one such as CrystFEL

19. Table of Contents Scope and objective Outcome of the review 2018
Status of work progress
Summary of authorized changes
Manpower
Risks and mitigation
Schedule and major upcoming milestones

20. Summary of authorized changes
IAU
wall
aperture
WBM
Pre-focus K-B
SSS
CRL
Focus K-B
sample
Optimization of optical layout
From two-step focusing to focus directly
Less number of optical elements (6/7 to 3/4)
Shorter whole length of beamline (78.7m to 53.4m)
Control software (GUI) has been identified (MXCuBE)
2018
31.5m m 45m m 50m m 52.9m m
undulator
Shielding wall
White slit
HDCM
CRL
VFM HFM sample
Mono slit
2019

21. Table of Contents Scope and objective Outcome of the review 2018
Status of work progress
Summary of authorized changes
Manpower
Risks and mitigation
Schedule and major upcoming milestones

22. Manpower

23. Table of Contents Scope and objective Outcome of the review 2018
Status of work progress
Summary of authorized changes
Manpower
Risks and mitigation
Schedule and major upcoming milestones

24. Risks and mitigation Risk ID Description Date Identified Likelihood
Risk Class
(severity)
Control Measure
Risk Owner
Status
Date Closed
BA-RI-01
the time for getting high quality KB mirror maybe longer than expected
2019/01
Medium
estimating the potential vender, such as Zeiss et al.
BA/Optical system
Ongoing
Not sure
BA-RI-02
monochromator will be self-developed, schedule maybe tight
more staffs
BA-RI-03
quality of CRL lens can not be controlled effectively
Low
test in advance, try to choose the product with reliable quality

25. Table of Contents Scope and objective Outcome of the review 2018
Status of work progress
Summary of authorized changes
Manpower
Risks and mitigation
Schedule and major upcoming milestones

26. Schedule and major coming milestone
the optical layout design frozen
the engineering design frozen
start to Experiment Hall alignment
start to install and commissioning the beamline equipment offline
start to beamline commissioning with X-ray beam
Class I CPM plan of MX beamline

27. Summary
Optimize the optical layout based on the recommendation of 2018 IAC committee
From two-step focusing to focus directly
Will replace the HDCM with HCCM
Identify the control software (MXCuBE)
The experimental method will focus on serial synchrotron crystallography (SSX)

28. Acknowledgement The support team
(optical, mechanics, control, engineering drawing etc)
SLS: Prof. Meitian Wang
SSRF: Prof. Jianhua He, Dr. Qisheng Wang, Dr. Bo Sun

29. Thank you for your attention!

30. Supporting material
Compare HEPS-MX beamline to others micro-focusing beamlines
HEPS-MX
MicroMAX（MAXIV）
VMXm
(Diamond)
BL02U
(SSRF)
BL32XU
(Spring-8)
ID29/EBSL8
(ESRF)
Energy range（keV）
5-18
5-30
7-25
7-15
9-15
10-30
Spot size
1-30
1-10
0.5-10
0.5-2
1-15
Energy resolution
2e-4
flux
7.0e13
1.0e13
~1.0e12
3.5e11
7e10
2e14
(0.3%BW)
status
Under design
In operation