5KGO
Structure of K. pneumonia MrkH-c-di-GMP complex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 298 | 20% PEG 3350, 0.1 M Bis tris propane/HCl pH 6.5, 0.2 M sodium fluoride. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.02 | 59.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.573 | α = 90 |
b = 74.569 | β = 90 |
c = 135.538 | 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 | CCD | ADSC QUANTUM 315r | 2016-01-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.11 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.9 | 37.285 | 94.1 | 5.2 | 3.2 | 14247 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.9 | 3.06 | 96.5 | 0.8 | 1.2 | 3.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MAD | FREE R-VALUE | 2.9 | 37.285 | 1.35 | 14120 | 1413 | 92.3 | 0.2318 | 0.2257 | 0.2887 | 97.68 |
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] | |
-12.8661 | 24.9129 | -12.0469 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 40.688 |
f_angle_d | 1.721 |
f_chiral_restr | 0.06 |
f_plane_restr | 0.045 |
f_bond_d | 0.028 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3688 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 184 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
SOLVE | phasing |
RESOLVE | model building |
PDB_EXTRACT | data extraction |