8I8N
Crystal structure of the ternary complex of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter sp. with Dephosphocoenzyme-A and Phosphonoacetic acid at 2.22 A resolution.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8I8I |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | BIS-TRIS propane pH 7.0, Sodium citrate tribasic dihydrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 54.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 137.268 | α = 90 |
b = 78.418 | β = 93.1 |
c = 106.465 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 2M | 2022-09-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.8731 | ESRF | ID23-2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.22 | 43.18 | 95.2 | 0.966 | 4.3 | 2.2 | 53025 | 33.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.22 | 2.28 | 0.239 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.22 | 43.147 | 52373 | 2635 | 93.617 | 0.239 | 0.2381 | 0.261 | 47.691 |
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] | |
0.005 | -0.008 | -0.01 | 0.006 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 14.339 |
r_dihedral_angle_3_deg | 14.221 |
r_lrange_other | 11.631 |
r_lrange_it | 11.63 |
r_dihedral_angle_2_deg | 11.612 |
r_scangle_it | 7.447 |
r_scangle_other | 7.446 |
r_dihedral_angle_1_deg | 6.73 |
r_mcangle_it | 6.559 |
r_mcangle_other | 6.558 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7547 |
Nucleic Acid Atoms | |
Solvent Atoms | 484 |
Heterogen Atoms | 146 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
MxCuBE | data collection |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |
Coot | model building |