7ZC3
Crystal structure of human copper chaperone Atox1 bound to zinc ion by CxxC motif
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4QOT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 293 | Drop:12.5mg/ml Atox1 + 1.62mM ZnSO4 in 25mM Sodium Phosphate buffer pH 7.0, 2mM DTT; Reservoir: 1.9M Li2SO4, 100mM MES pH 6.0, 2.5% glycerol; VAPOR DIFFUSION, SITTING DROP, temperature 293K. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.26 | 62.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.226 | α = 90 |
b = 78.226 | β = 90 |
c = 54.637 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 | 80 | PIXEL | DECTRIS EIGER2 S 16M | 2021-11-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 1.2800 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.9 | 39.04 | 94.3 | 0.998 | 14.6 | 2.3 | 23876 | 27.48 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.9 | 1.94 | 92 | 0.765 |
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 | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4qot | 1.9 | 25.61 | 1.36 | 23876 | 1214 | 81.65 | 0.1662 | 0.165 | 0.1859 | 32.4581 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1012 |
Nucleic Acid Atoms | |
Solvent Atoms | 141 |
Heterogen Atoms | 31 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
XDS | data reduction |
Aimless | data scaling |
Sir2014 | phasing |
PHENIX | model building |
PHENIX | refinement |
PDB_EXTRACT | data extraction |