4XGV
Crystal structure of Escherichia coli Flavin trafficking protein, an FMN transferase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2O18 | PDB ENTRY 2O18 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 0.2 M ammonium nitrate, 20% (w/v) PEG 3350, 35% (v/v) ethylene glycol; |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.99 | 38.31 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 56.197 | ¦Á = 75.7 |
b = 70.645 | ¦Â = 72.45 |
c = 85.961 | ¦Ã = 69.28 |
Symmetry | |
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Space Group | P 1 |
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 | monochromator | 2012-03-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97918 | APS | 19-ID |
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 | 1.88 | 50 | 96.9 | 0.064 | 7.6 | 2.1 | 91038 | 91038 | 21.44 |
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 | 1.88 | 1.91 | 94.5 | 0.581 | 1.8 | 2.1 | 4488 |
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 | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | FREE R-VALUE | PDB ENTRY 2O18 | 1.883 | 31.513 | 1.97 | 90846 | 4544 | 96.37 | 0.1645 | 0.1626 | 0.2008 | random selection | 34.2088 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.692 |
f_angle_d | 0.956 |
f_chiral_restr | 0.037 |
f_bond_d | 0.007 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9514 |
Nucleic Acid Atoms | |
Solvent Atoms | 776 |
Heterogen Atoms | 143 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data reduction |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data scaling |
PHENIX | phasing |