7C8H

Ambient temperature structure of Bifidobacterium longum phosphoketolase with thiamine diphosphate

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		298	Equal amount of 15 mg ml-1 PKT solution (4 mM DTT, 10 mg ml-1 ThDpp) and precipitant solution (50 mM malonate, 12% tacsimate (pH5), 17% PEG3350) were mixed in order to prepare seed crystals. Preparations of seed crystals of PKT were performed by utilizing light induced crystallization method which promoted to form initial crystal nucleus by evanescent field arised from light irradiation to gold nano-particle vapored on general polystyrene plate (Fujifilm Wako). After 16 h, precipitated crystals were homogenized and centrifuged to use supernatant as seed solution. For the purpose of forming micro-sized crystals of PKT, 1176 micro l of protein-precipitant solution mixture as the same components of seed crystals preparation was mixed with 120 micro l of the seed solution in a 1.5 ml tube. After gentle rotation at 25 degree C for 2 h, the supernatant was exchanged to the same precipitant solution. The same buffer exchange was iteratively conducted after 10 h and 16 h.

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.62	α = 90
b = 185.8	β = 99.61
c = 162.89	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	CCD	MPCCD		2016-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL3	1.7714	SACLA	BL3

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (All)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.5	46.8	100	0.938	0.215	3.64	234		292114			57.854

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	100		0.493	1.006	1.11	165.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3AI7	2.5	46.8	277500	14633	99.98	0.1642	0.1613	0.2176	RANDOM	54.255

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.9		-0.48	-1		1.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.25
r_dihedral_angle_4_deg	18.65
r_dihedral_angle_3_deg	17.076
r_dihedral_angle_1_deg	7.56
r_angle_refined_deg	1.582
r_angle_other_deg	1.277
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	51353
Nucleic Acid Atoms
Solvent Atoms	1106
Heterogen Atoms	279

Software

Software
Software Name	Purpose
REFMAC	refinement
Cheetah	data collection
CrystFEL	data processing
MOLREP	phasing
Coot	model building
CrystFEL	data reduction
CrystFEL	data scaling