8CJ0
E. coli NfsB-T41Q/N71S/F124T/M127V mutant bound to nicotinate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ICR | wild type NfsB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 291 | 12% PEG 4000, 100 mM Na Acetate, 20 mM Nicotinic acid, 15% Ethylene glycol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.19 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 57.31 | ¦Á = 90 |
b = 57.31 | ¦Â = 90 |
c = 265.67 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 41 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 | CCD | ADSC QUANTUM 210r | 2009-07-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.934 | ESRF | ID14-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.99 | 35.06 | 98.9 | 0.075 | 25.3 | 9 | 31129 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.994 | 2.046 | 95.4 | 0.55 | 8.93 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.99 | 35.06 | 29553 | 1575 | 98.88 | 0.16283 | 0.16095 | 0.19869 | RANDOM | 38.944 |
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] | |
-0.04 | -0.04 | 0.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 13.675 |
r_long_range_B_other | 11.808 |
r_long_range_B_refined | 11.792 |
r_scangle_other | 10.176 |
r_scbond_other | 7.44 |
r_scbond_it | 7.438 |
r_dihedral_angle_1_deg | 6.123 |
r_mcangle_other | 5.442 |
r_mcangle_it | 5.425 |
r_mcbond_it | 4.057 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3344 |
Nucleic Acid Atoms | |
Solvent Atoms | 154 |
Heterogen Atoms | 84 |
Software
Software | |
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Software Name | Purpose |
PDB-REDO | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
PHENIX | phasing |