5JPD
Metal ABC transporter from Listeria monocytogenes with cadmium
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5HX7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 289 | 0.2 M magnesium chloride, 0.02 M cadmium chloride, 0.1 M Tris buffer, 20% PEG 8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.87 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.316 | α = 90 |
b = 62.341 | β = 90 |
c = 75.987 | 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 | CCD | ADSC QUANTUM 210r | 2016-02-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.9792 | APS | 19-BM |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.72 | 28.3 | 98.4 | 0.093 | 16.5 | 5.1 | 29346 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.72 | 1.75 | 91 | 0.549 | 2.02 | 2.8 |
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 | 5HX7 | 1.72 | 28.2 | 27830 | 1460 | 98.34 | 0.1688 | 0.1669 | 0.2071 | RANDOM | 25.245 |
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] | |
1.2 | -1.35 | 0.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.842 |
r_dihedral_angle_4_deg | 14.545 |
r_dihedral_angle_3_deg | 13.44 |
r_dihedral_angle_1_deg | 5.992 |
r_mcangle_it | 1.773 |
r_angle_refined_deg | 1.291 |
r_mcbond_it | 1.092 |
r_mcbond_other | 1.087 |
r_angle_other_deg | 0.759 |
r_chiral_restr | 0.075 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2204 |
Nucleic Acid Atoms | |
Solvent Atoms | 233 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
HKL-3000 | phasing |