Cry3A Toxin structure obtained by injecting Bacillus thuringiensis cells in an XFEL beam, collecting data by serial femtosecond crystallographic methods and processing data with the CrystFEL software suite
Components
Pesticidal crystal protein cry3Aa
Keywords
TOXIN / in vivo crystals / microcrystals / serial femtosecond crystallography / SFX / LCLS / X-ray Free-electron laser / insecticidal toxin
Function / homology
Function and homology information
symbiont-mediated killing of host cell / sporulation resulting in formation of a cellular spore / toxin activity / signaling receptor binding Similarity search - Function
Monochromator: no monochromator, FEL beam with 20-30 eV bandwidth Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.457 Å / Relative weight: 1
Reflection
Resolution: 2.9→88.64 Å / Num. all: 18944 / Num. obs: 18944 / % possible obs: 100 % / Redundancy: 484.3 % / Biso Wilson estimate: 94.61 Å2 / Rmerge(I) obs: 0.244 / Net I/σ(I): 5.2
Reflection shell
Resolution: 2.9→3 Å / Redundancy: 444.5 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 0.8 / % possible all: 100
-
Processing
Software
Name
Version
Classification
NB
BUSTER-TNT
refinement
PDB_EXTRACT
3.14
dataextraction
CrystFEL
datareduction
CrystFEL
datascaling
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.9→44.31 Å / Cor.coef. Fo:Fc: 0.9532 / Cor.coef. Fo:Fc free: 0.9462 / SU R Cruickshank DPI: 2.03 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.327 / SU Rfree Blow DPI: 0.271 / SU Rfree Cruickshank DPI: 0.279 / Stereochemistry target values: Engh & Huber
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.194
931
4.92 %
RANDOM
Rwork
0.1772
-
-
-
obs
0.178
18934
99.99 %
-
all
-
18934
-
-
Displacement parameters
Biso mean: 83.9 Å2
Baniso -1
Baniso -2
Baniso -3
1-
8.3562 Å2
0 Å2
0 Å2
2-
-
10.2736 Å2
0 Å2
3-
-
-
-18.6298 Å2
Refine analyze
Luzzati coordinate error obs: 0.389 Å
Refinement step
Cycle: LAST / Resolution: 2.9→44.31 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4659
0
0
0
4659
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
4782
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.02
6511
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1612
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
124
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
694
HARMONIC
5
X-RAY DIFFRACTION
t_it
4782
HARMONIC
50
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.55
X-RAY DIFFRACTION
t_other_torsion
18.96
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
618
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
5225
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.9→3.06 Å / Total num. of bins used: 10
Rfactor
Num. reflection
% reflection
Rfree
0.285
141
5.18 %
Rwork
0.2646
2581
-
all
0.2657
2722
-
obs
-
-
99.99 %
Refinement TLS params.
Method: refined / Origin x: 36.3567 Å / Origin y: 42.6079 Å / Origin z: 46.6911 Å
11
12
13
21
22
23
31
32
33
T
-0.1127 Å2
0.0057 Å2
0.031 Å2
-
-0.0494 Å2
-0.0326 Å2
-
-
-0.125 Å2
L
1.453 °2
0.5359 °2
0.4753 °2
-
0.9441 °2
0.2678 °2
-
-
0.5393 °2
S
-0.0207 Å °
0.0999 Å °
-0.3544 Å °
-0.0703 Å °
0.144 Å °
-0.1627 Å °
0.0055 Å °
-0.022 Å °
-0.1233 Å °
Refinement TLS group
Selection details: { A|* }
+
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