2CMN
A Proximal Arginine Residue in the Switching Mechanism of the FixL Oxygen Sensor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1LSW | PDB ENTRY 1LSW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 277 | CRYSTALS OF THE MET-R206A BJFIXLH MUTANT WERE OBTAINED AT 4 DEGREES C VIA THE HANGING-DROP VAPOR-DIFFUSION METHOD BY MIXING EQUAL AMOUNTS OF PROTEIN (0.6-1.2 MM IN 5.0 MM TRIS-HCL, PH 8.0) AND WELL SOLUTION (50 MM HEPES, 4.5 M NACL, 5% (V/) 2-METHYL-2,4-PENTANEDIOL, PH 7.5) AND INCUBATING THE DROP OVER 0.7 ML OF WELL SOLUTION. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.25 | 61.89 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 127.117 | α = 90 |
b = 127.117 | β = 90 |
c = 58.569 | γ = 120 |
Symmetry | |
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Space Group | H 3 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 | CUSTOM | 2003-10-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | APS | 19-BM |
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 | 2.3 | 27.07 | 99.9 | 0.06 | 36.2 | 7.4 | 8187 | -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 | 2.3 | 2.34 | 100 | 0.74 | 2.9 | 6.3 |
Refinement
Statistics | |||||||||||||||||||
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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 | PDB ENTRY 1LSW | 2.3 | 20 | 7565 | 611 | 99.9 | 0.197 | 0.195 | 0.22 | RANDOM | 41.23 |
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] | |
0.45 | 0.22 | 0.45 | -0.67 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.8 |
r_dihedral_angle_4_deg | 18.68 |
r_dihedral_angle_3_deg | 16.975 |
r_scangle_it | 2.476 |
r_dihedral_angle_1_deg | 2.006 |
r_angle_refined_deg | 1.693 |
r_scbond_it | 1.69 |
r_mcangle_it | 1.093 |
r_mcbond_it | 0.721 |
r_nbtor_refined | 0.301 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 924 |
Nucleic Acid Atoms | |
Solvent Atoms | 33 |
Heterogen Atoms | 43 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |