5NC4
Crystal structure of the ferric enterobactin receptor (PfeA) in complex with protochelin from Pseudomonas aeruginosa
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5M9K |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 6.5 | 294 | PEG 8000, ADA, Magnesium acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.39 | 63.66 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 86.751 | ¦Á = 90 |
b = 157.352 | ¦Â = 90 |
c = 78.108 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 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 PILATUS3 6M | 2016-04-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.9686 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.8 | 157.35 | 100 | 0.054 | 0.999 | 19.5 | 7.2 | 26955 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.8 | 2.813 | 97.6 | 0.695 | 0.867 | 2.3 | 7.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 5M9K | 2.8 | 78.68 | 25602 | 1310 | 99.93 | 0.22026 | 0.21811 | 0.26326 | RANDOM | 110.265 |
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] | |
2.46 | 2.15 | -4.61 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.952 |
r_dihedral_angle_3_deg | 17.1 |
r_dihedral_angle_4_deg | 16.549 |
r_long_range_B_refined | 11.031 |
r_long_range_B_other | 11.031 |
r_dihedral_angle_1_deg | 9.506 |
r_scangle_other | 8.398 |
r_mcangle_it | 7.583 |
r_mcangle_other | 7.536 |
r_scbond_it | 6.095 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5363 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |