2IQQ
The Crystal Structure of Iron, Sulfur-Dependent L-serine dehydratase from Legionella pneumophila subsp. pneumophila
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | 50 mM Ammonium sulfate, 50 mM Bis-tris pH 6.5, 30 % Pentaerythritol ethoxylate, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.24 | 62.01 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 120.705 | α = 90 |
b = 77.151 | β = 117.91 |
c = 56.158 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 315 | mirrors | 2006-06-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 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 | 2.66 | 38.58 | 98.6 | 0.104 | 10.1 | 8.3 | 12986 | 12986 |
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 | 2.66 | 2.76 | 93 | 0.665 | 1.9 | 4.9 |
Refinement
Statistics | |||||||||||||||||||
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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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.66 | 38.58 | 11671 | 11671 | 1280 | 98.33 | 0.17957 | 0.17435 | 0.2259 | RANDOM | 69.511 |
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] | |
-0.84 | -0.02 | 2.24 | -1.42 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.304 |
r_dihedral_angle_3_deg | 22.327 |
r_dihedral_angle_4_deg | 19.113 |
r_dihedral_angle_1_deg | 11.776 |
r_scangle_it | 3.5 |
r_scbond_it | 2.131 |
r_angle_refined_deg | 1.736 |
r_mcangle_it | 1.421 |
r_mcbond_it | 0.776 |
r_symmetry_vdw_refined | 0.291 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2258 |
Nucleic Acid Atoms | |
Solvent Atoms | 63 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SBC-Collect | data collection |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
HKL-3000 | phasing |
SHELXCD | phasing |
SHELXD | phasing |
SHELXE | model building |
MLPHARE | phasing |
SOLVE | phasing |
RESOLVE | phasing |
PHENIX | phasing |