6DT4
1.8 Angstrom Resolution Crystal Structure of cAMP-Regulatory Protein from Yersinia pestis in Complex with cAMP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3RYP | PDB entry 3RYP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 292 | 6.6 mg/mL protein, 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3, 1 mM cAMP against PACT (H12) (0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 8.5, 20% w/v PEG3350) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 50.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.876 | α = 90 |
b = 82.8 | β = 90 |
c = 106.35 | 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 | RAYONIX MX-300 | C(111) | 2018-06-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.8 | 30 | 99.1 | 0.058 | 0.058 | 0.062 | 0.021 | 30.5 | 8.5 | 44393 | -3 | 29.9 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 1.8 | 1.83 | 97.3 | 0.722 | 0.722 | 0.776 | 0.278 | 0.874 | 2.9 | 7.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | PDB entry 3RYP | 1.8 | 29.61 | 42181 | 2168 | 99.03 | 0.1761 | 0.17481 | 0.20304 | RANDOM | 41.444 |
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] | |
-2.31 | 3.41 | -1.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.591 |
r_dihedral_angle_4_deg | 15.577 |
r_dihedral_angle_3_deg | 10.502 |
r_long_range_B_refined | 6.792 |
r_long_range_B_other | 6.698 |
r_scangle_other | 4.51 |
r_dihedral_angle_1_deg | 3.986 |
r_mcangle_it | 2.928 |
r_mcangle_other | 2.928 |
r_scbond_it | 2.83 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3181 |
Nucleic Acid Atoms | |
Solvent Atoms | 292 |
Heterogen Atoms | 47 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
MoRDa | phasing |