6TMU
Crystal structure of the chaperonin gp146 from the bacteriophage EL 2 (Pseudomonas aeruginosa) in presence of ATP-BeFx, crystal form II
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 8 | 293 | 8 % PEG-6000, 0.15 M NaCl and 0.1 M Tris-HCl pH 8.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.34 | 63.14 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 145.516 | α = 90 |
b = 151.461 | β = 90 |
c = 261.347 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2018-04-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 0.8500 | ESRF | ID30B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 3.54 | 49.47 | 99.8 | 0.111 | 0.125 | 0.056 | 0.997 | 7.9 | 4.9 | 70880 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 3.54 | 3.62 | 99.9 | 1.119 | 1.255 | 0.557 | 0.465 | 4.9 |
Refinement
Statistics | |||||||||||||||||||
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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 | EMD-6492 | 3.54 | 30 | 67159 | 3576 | 99.51 | 0.2516 | 0.2504 | 0.2747 | RANDOM | 170.101 |
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] | |
0.38 | 1.36 | -1.74 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.559 |
r_dihedral_angle_3_deg | 13.241 |
r_dihedral_angle_4_deg | 10.922 |
r_dihedral_angle_1_deg | 5.054 |
r_angle_refined_deg | 0.967 |
r_angle_other_deg | 0.865 |
r_chiral_restr | 0.051 |
r_bond_refined_d | 0.005 |
r_bond_other_d | 0.003 |
r_gen_planes_refined | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 29093 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 213 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |