7TCM
Crystal Structure of aspartate-semialdehyde dehydrogenase from Acinetobacter baumannii in complex with NADP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7SKB | apo structure, pdb entry 7SKB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 287 | Molecular Dimensions/Calibre MCSG1 screen, condition B3: 200mM Ammonium acetate,100mM BisTris / HCl pH 5.5, 25% (w/V) PEG 3350: AcbaC.17885.a.B1.PW38925 at 18mg/ml + 3mM NADP: additionally soaked over night with 5mM NADP: tray 3420159 b5: 15% EG + soak: puck: xdl8-1. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.95 | α = 90 |
b = 53.21 | β = 102.358 |
c = 87.33 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | Beryllium Lenses | 2021-11-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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) | Rrim 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 | 1.95 | 50 | 97.4 | 0.043 | 0.05 | 0.998 | 18.42 | 3.498 | 53292 | 33.934 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.95 | 2 | 80.9 | 0.191 | 0.249 | 0.945 | 4.3 | 2.34 |
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 | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | apo structure, pdb entry 7SKB | 1.95 | 45.15 | 1.35 | 53273 | 2023 | 97.48 | 0.1528 | 0.1516 | 0.1842 | 0 | 36 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.3101 |
f_angle_d | 0.8217 |
f_chiral_restr | 0.0542 |
f_bond_d | 0.0068 |
f_plane_restr | 0.0068 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5608 |
Nucleic Acid Atoms | |
Solvent Atoms | 509 |
Heterogen Atoms | 96 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |
Coot | model building |
PHENIX | model building |