6TTS
Crystal structure of the GGDEF domain of DgcB from Caulobacter crescentus in complex with c-di-GMP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3IGN | 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme |
experimental model | PDB | 3HVA | 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme |
experimental model | PDB | 3QYY | 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme |
experimental model | PDB | 3I5C | 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme |
experimental model | PDB | 4WXW | 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme |
experimental model | PDB | 3TVK | 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme |
experimental model | PDB | 4URG | 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme |
experimental model | PDB | 4ZVF | 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme |
experimental model | PDB | 4H54 | 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme |
experimental model | PDB | 4ZMM | 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme |
experimental model | PDB | 3ICL | 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme |
experimental model | PDB | 4IOB | 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme |
experimental model | PDB | 5EUH | 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme |
experimental model | PDB | 3EZU | 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme |
experimental model | PDB | 4YME | 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | 0.2 M LiSO4, 0.1 M NaAcet pH 5.5, 8% w/v PEG 20k, 8% v/v PEG 500 MME, 500 uM c-di-GMP, 1 mM GTP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.99 | 58.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.5 | α = 90 |
b = 64.5 | β = 90 |
c = 246.76 | γ = 90 |
Symmetry | |
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Space Group | P 41 2 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 | PIXEL | DECTRIS EIGER X 16M | 2018-06-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 0.97947 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.5 | 64.5 | 99.9 | 0.159 | 0.183 | 0.088 | 0.813 | 8.3 | 7.2 | 19045 | 29.29 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.5 | 2.6 | 99 | 0.515 | 0.672 | 0.427 | 0.693 | 2.3 | 3.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | FREE R-VALUE | 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme | 2.5 | 50.76 | 1.34 | 18974 | 1002 | 99.8 | 0.2065 | 0.2035 | 0.2608 | 29.68 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 26.9272 |
f_angle_d | 1.3588 |
f_chiral_restr | 0.0664 |
f_bond_d | 0.0098 |
f_plane_restr | 0.0063 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2645 |
Nucleic Acid Atoms | |
Solvent Atoms | 16 |
Heterogen Atoms | 260 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
iMOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |