7QA1 | pdb_00007qa1

The structure of natural crystals of the Lysinibacillus sphaericus Tpp49Aa1 pesticidal protein elucidated using serial femtosecond crystallography at an X-ray free electron laser

X-RAY DIFFRACTION

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Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WA1	3WA1, 5FOY, 5G37
experimental model	PDB	5FOY	3WA1, 5FOY, 5G37
experimental model	PDB	5G37	3WA1, 5FOY, 5G37

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	IN CELL		298	Natural crystallisation

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.76	α = 90
b = 83.15	β = 90
c = 157.33	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	AGIPD		2021-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	EUROPEAN XFEL BEAMLINE SPB/SFX	1.33	European XFEL	SPB/SFX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	Double flow focusing nozzle (DFFN)	injection

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1	3D printed DFFN (CFEL)	undefined (µl/min)	undefined (µm)		DFFN

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	2.2	28.57	100	0.99	0.12	8.91	485		53943

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	2.2	2.22	100		0.48	0.918	1.25	28.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3WA1, 5FOY, 5G37	2.2	28.57	52112	1755	99.93	0.1611	0.1599	0.1671	0.1967	0.1977	RANDOM	31.759

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]
-0.07			0.58		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.592
r_dihedral_angle_4_deg	18.811
r_dihedral_angle_3_deg	14.739
r_dihedral_angle_1_deg	7.533
r_angle_refined_deg	1.848
r_angle_other_deg	1.321
r_chiral_restr	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6748
Nucleic Acid Atoms
Solvent Atoms	370
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing
PHENIX	refinement
PHENIX	model building