8ZN4
Crystal structure of Poly(ethylene glycol) stabilized erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii at 2.30 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3CMC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 7.5 | 298 | A reservoir solution containing 0.2 M MgCl2.6H2O, 0.1 M HEPES sodium (pH 7.5), and 30% v/v PEG 400 was prepared. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3 | 59.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 145.775 | α = 90 |
b = 167.135 | β = 90 |
c = 150.103 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | 298 | PIXEL | DECTRIS EIGER2 X 9M | 2023-07-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 0.87313 | ESRF | ID30B |
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 | 2.3 | 46.703 | 100 | 0.2 | 0.02 | 0.06 | 0.998 | 11.2 | 13.2 | 81357 |
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 | 2.3 | 2.34 | 100 | 1.58 | 1.69 | 0.47 | 0.82 | 2.2 | 12.6 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3CMC | 2.3 | 46.703 | 81321 | 2400 | 99.963 | 0.153 | 0.1517 | 0.201 | 44.028 |
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] | |
1.561 | -3.614 | 2.053 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 14.571 |
r_dihedral_angle_3_deg | 13.205 |
r_lrange_it | 9.593 |
r_lrange_other | 9.584 |
r_dihedral_angle_2_deg | 8.827 |
r_scangle_it | 7.528 |
r_scangle_other | 7.528 |
r_dihedral_angle_1_deg | 7.008 |
r_mcangle_it | 5.144 |
r_mcangle_other | 5.143 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10716 |
Nucleic Acid Atoms | |
Solvent Atoms | 641 |
Heterogen Atoms | 488 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |
Coot | model building |