5TPI
1.47 Angstrom Crystal Structure of the C-terminal Substrate Binding Domain of LysR Family Transcriptional Regulator from Klebsiella pneumoniae.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 295 | Protein: 18.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES pH 7.5, Screen: 3.2M NaCl, 0.1M Bis-Tris-propane (pH=7.0); Cryo: Paratone. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.756 | α = 90 |
b = 40.228 | β = 129.41 |
c = 68.211 | 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 | MARMOSAIC 300 mm CCD | C(111) | 2016-10-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.47 | 30 | 99.6 | 0.037 | 0.037 | 35.8 | 4.5 | 33672 | -3 | 13.9 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.47 | 1.5 | 99.7 | 0.638 | 0.837 | 2.3 | 4.3 |
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 | SAD | THROUGHOUT | 1.47 | 26.35 | 31890 | 1662 | 99.62 | 0.13886 | 0.13674 | 0.1806 | RANDOM | 25.584 |
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] | |
0.52 | -0.65 | 4.16 | -1.53 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.108 |
r_sphericity_free | 25.406 |
r_dihedral_angle_4_deg | 11.638 |
r_dihedral_angle_3_deg | 11.407 |
r_sphericity_bonded | 11.346 |
r_dihedral_angle_1_deg | 4.15 |
r_long_range_B_refined | 3.932 |
r_long_range_B_other | 3.431 |
r_scangle_other | 2.845 |
r_scbond_it | 2.366 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1592 |
Nucleic Acid Atoms | |
Solvent Atoms | 208 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHENIX | phasing |