3FWZ
Crystal structure of TrkA-N domain of inner membrane protein ybaL from Escherichia coli
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 297 | 0.2 M MgCl2, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.52 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 34.801 | ¦Á = 90 |
b = 53.071 | ¦Â = 97.82 |
c = 72.537 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM Q315r | 2008-12-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97926 | 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 | 1.79 | 50 | 99.8 | 0.063 | 47 | 4.9 | 24693 | 24652 | -3 | 20.6 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.8 | 1.82 | 100 | 0.196 | 11.65 | 4.4 | 620 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.79 | 50 | 24633 | 24633 | 1259 | 98.44 | 0.16968 | 0.16968 | 0.16787 | 0.20159 | RANDOM | 17.469 |
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] | |
1.16 | 0.13 | -0.77 | -0.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.354 |
r_dihedral_angle_4_deg | 18.612 |
r_dihedral_angle_3_deg | 13.405 |
r_dihedral_angle_1_deg | 5.178 |
r_scangle_it | 3.706 |
r_scbond_it | 2.297 |
r_angle_refined_deg | 1.47 |
r_mcangle_it | 1.284 |
r_mcbond_it | 0.702 |
r_chiral_restr | 0.094 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2100 |
Nucleic Acid Atoms | |
Solvent Atoms | 201 |
Heterogen Atoms | 47 |
Software
Software | |
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Software Name | Purpose |
SBC-Collect | data collection |
HKL-3000 | phasing |
MLPHARE | phasing |
DM | model building |
SHELXD | phasing |
RESOLVE | model building |
Coot | model building |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
DM | phasing |
RESOLVE | phasing |