7C8I

Ambient temperature structure of Bifidobacgterium longum phosphoketolase with thiamine diphosphate and phosphoenol pyuruvate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AI7

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, 140 mM PEP) were mixed in order to prepare seed crystals. 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	57.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.3	α = 90
b = 184.94	β = 99.18
c = 163.13	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		2016-10-13	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	48.1	100	0.96	0.181	4.16	486.3		292114

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		0.411	1.135	1.06	343.7

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	48.1	278240	14508	99.91	0.169	0.1661	0.2257	RANDOM	56.253

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]
		-0.54	-1.4		1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.51
r_dihedral_angle_4_deg	18.732
r_dihedral_angle_3_deg	17.532
r_dihedral_angle_1_deg	7.779
r_angle_refined_deg	1.63
r_angle_other_deg	1.272
r_chiral_restr	0.069
r_bond_refined_d	0.009
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	51417
Nucleic Acid Atoms
Solvent Atoms	1022
Heterogen Atoms	296

Software

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