4E1T
X-ray crystal structure of the transmembrane beta-domain from invasin from Yersinia pseudotuberculosis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4E1S | PDB ENTRY 4E1S |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIPIDIC CUBIC PHASE MONOOLEIN | 4 | 294 | 0.05 M sodium citrate, pH 3.8-4.4, 0.2 M lithium sulfate, 23-35% PEG400, LIPIDIC CUBIC PHASE MONOOLEIN, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.9 | 57.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.404 | α = 90 |
b = 124.885 | β = 90 |
c = 65.073 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | MARMOSAIC 300 mm CCD | K-B pair of biomorph mirrors | 2011-06-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1.034375 | APS | 23-ID-B |
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 | 2.263 | 67.007 | 92.7 | 0.133 | 8.2 | 5.1 | 15222 | 14111 | 2.3 | 2.3 |
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 | 2.263 | 2.38 | 76.2 | 0.599 | 2.9 | 1133 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4E1S | 2.263 | 29.787 | 15222 | 14016 | 709 | 90.55 | 0.1915 | 0.1915 | 0.188 | 0.2596 | RANDOM | 50.288 |
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] | |
1.46 | 1.15 | -2.61 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 42.565 |
r_dihedral_angle_4_deg | 21.553 |
r_dihedral_angle_3_deg | 17.787 |
r_dihedral_angle_1_deg | 6.926 |
r_scangle_it | 3.913 |
r_scbond_it | 2.566 |
r_angle_refined_deg | 1.954 |
r_mcangle_it | 1.444 |
r_mcbond_it | 0.782 |
r_chiral_restr | 0.13 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1960 |
Nucleic Acid Atoms | |
Solvent Atoms | 117 |
Heterogen Atoms | 283 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Blu-Ice | data collection |