4XSJ
Crystal structure of the N-terminal domain of the human mitochondrial calcium uniporter fused with T4 lysozyme
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2LZM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | 20% PEG 3350, 5% glycerol, 0.3 M ammonium sulphate and 0.1 M Bis-Tris-HCl (pH 5.5) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.91 | 57.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 98.085 | α = 90 |
b = 98.085 | β = 90 |
c = 62.409 | 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 | 100 | CCD | ADSC QUANTUM 315r | 2013-12-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PAL/PLS BEAMLINE 5C (4A) | 0.9795 | PAL/PLS | 5C (4A) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.65 | 50 | 97.9 | 15.9 | 7.2 | 32604 |
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 | 2LZM | 1.8 | 48.5 | 29581 | 1536 | 98.2 | 0.13 | 0.127 | 0.19 | RANDOM | 29.253 |
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] | |
0.59 | 0.3 | 0.59 | -1.92 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 48.541 |
r_dihedral_angle_2_deg | 34.393 |
r_sphericity_bonded | 21.789 |
r_dihedral_angle_4_deg | 12.689 |
r_dihedral_angle_3_deg | 11.764 |
r_long_range_B_refined | 6.757 |
r_long_range_B_other | 4.917 |
r_dihedral_angle_1_deg | 4.74 |
r_scangle_other | 3.59 |
r_mcangle_it | 3.164 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2008 |
Nucleic Acid Atoms | |
Solvent Atoms | 431 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Coot | model building |
HKL-2000 | data processing |