5IDM
Bifunctional histidine kinase CckA (domain, CA) in complex with c-di-GMP and AMPPNP/Mg2+
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 277 | 0.1 M ammonium sulfate, 28.4% polyethylene glycol 4000 and 0.1 M MES pH 5.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.28 | α = 90 |
b = 62.11 | β = 90 |
c = 103.89 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | PIXEL | DECTRIS PILATUS 2M | 2015-08-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 0.9999 | SLS | X06DA |
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 | 1.9 | 30 | 99.2 | 0.088 | 13.8 | 6.4 | 29150 |
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 | 1.9 | 2 | 99.3 | 0.3 | 2.5 | 6.5 |
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 | 1.9 | 30 | 27618 | 1492 | 98.98 | 0.1953 | 0.1935 | 0.2289 | RANDOM | 16.367 |
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] | |
-0.26 | -0.21 | 0.47 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.238 |
r_dihedral_angle_3_deg | 12.859 |
r_dihedral_angle_4_deg | 11.993 |
r_dihedral_angle_1_deg | 6.648 |
r_mcangle_it | 1.659 |
r_angle_refined_deg | 1.628 |
r_angle_other_deg | 1.276 |
r_mcbond_it | 0.948 |
r_mcbond_other | 0.948 |
r_chiral_restr | 0.086 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2735 |
Nucleic Acid Atoms | |
Solvent Atoms | 406 |
Heterogen Atoms | 110 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |