- PDB-4qx0: Cry3A Toxin structure obtained by Serial Femtosecond Crystallogra... -
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Open data
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Basic information
Entry
Database: PDB / ID: 4qx0
Title
Cry3A Toxin structure obtained by Serial Femtosecond Crystallography from in vivo grown crystals isolated from Bacillus thuringiensis and data processed with the cctbx.xfel 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: 1.454 Å / Relative weight: 1
Reflection
Resolution: 2.8→56.748 Å / Num. all: 19894 / Num. obs: 19894 / % possible obs: 95.6 % / Redundancy: 717.8 % / Biso Wilson estimate: 30.29 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 101.2
Reflection shell
Resolution: 2.8→2.88 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 1.8 / % possible all: 55.7
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Processing
Software
Name
Version
Classification
NB
BUSTER-TNT
refinement
PDB_EXTRACT
3.14
dataextraction
cctbx.xfel
datareduction
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→56.748 Å / Cor.coef. Fo:Fc: 0.9211 / Cor.coef. Fo:Fc free: 0.8931 / SU R Cruickshank DPI: 0.944 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.821 / SU Rfree Blow DPI: 0.257 / SU Rfree Cruickshank DPI: 0.264 / Stereochemistry target values: Engh & Huber
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1918
973
4.89 %
RANDOM
Rwork
0.165
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-
-
obs
0.1663
19894
95.65 %
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all
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19894
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-
Displacement parameters
Biso mean: 38.37 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.2472 Å2
0 Å2
0 Å2
2-
-
6.1529 Å2
0 Å2
3-
-
-
-4.9057 Å2
Refine analyze
Luzzati coordinate error obs: 0.339 Å
Refinement step
Cycle: LAST / Resolution: 2.8→56.748 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4659
0
0
26
4685
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
1.01
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
2.56
X-RAY DIFFRACTION
t_other_torsion
19.1
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
5399
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.8→2.95 Å / Total num. of bins used: 10
Rfactor
Num. reflection
% reflection
Rfree
0.3082
96
4.6 %
Rwork
0.2818
1990
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all
0.2831
2086
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obs
-
-
95.65 %
Refinement TLS params.
Method: refined / Origin x: 36.2681 Å / Origin y: 42.4623 Å / Origin z: 46.678 Å
11
12
13
21
22
23
31
32
33
T
-0.1479 Å2
0.007 Å2
0.0799 Å2
-
-0.0793 Å2
-0.0475 Å2
-
-
0.0886 Å2
L
2.1665 °2
0.6743 °2
0.7377 °2
-
0.8803 °2
0.1858 °2
-
-
0.6141 °2
S
-0.0842 Å °
0.174 Å °
-0.6825 Å °
-0.1047 Å °
0.25 Å °
-0.1757 Å °
-0.0711 Å °
-0.0095 Å °
-0.1658 Å °
Refinement TLS group
Selection details: { A|* }
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