4PJ1
Crystal structure of the human mitochondrial chaperonin symmetrical 'football' complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1AON |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 303 | Protein concentration: mHsp60, 9.5 mg/ml ; mHsp10, 1.6 mg/ml; Composition of protein solution: 50 mM Tris-HCl pH 7.7, 300 mM NaCl, 5% glycerol, 15 mM MgCl2, 0.5 mM KCl,1 mM ATP; Composition of reservoir solution: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dehydrate,30-35%(v/v) PEG 400 Volume and ratio of drop:5 micro l (1:1) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.29 | 62.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 199.1 | α = 90 |
b = 199.1 | β = 90 |
c = 627.39 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | 2013-12-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.95370 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (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 | 3.15 | 49.78 | 99.8 | 0.136 | 0.058 | 9 | 6.2 | 217130 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.15 | 3.26 | 99.1 | 1.491 | 0.793 | 0.7 | 4.1 | 20886 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | 1AON | 3.15 | 49.775 | 1.34 | 215814 | 10844 | 99.28 | 0.2422 | 0.2407 | 0.2704 | RANDOM | 121.1628 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.178 |
f_angle_d | 1.109 |
f_chiral_restr | 0.041 |
f_bond_d | 0.004 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 65571 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 392 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
PDB_EXTRACT | data extraction |
MOLREP | phasing |
PHENIX | refinement |
XSCALE | data scaling |
Aimless | data scaling |