7K5Z
Crystal Structure of Argininosuccinate synthase from Legionella pneumophila Philadelphia 1 in complex with ANPPNP and a substrate analogue Arginine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6XNQ | apo structure, pdb entry 6XNQ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 287 | Microlytic MCSG1 screen C5: 200mM MgOAc2, 20% (w/V) PEG 3350: LepnA.00809.a.B1.PS38414 + 3.5mM of each AMPPNP, Arginine, MgCl2: tray 316695 c5: cryo: 20% EG + 3.5mm AmPPNP and Arginine: puck iyy7-9 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 122.23 | α = 90 |
b = 103.54 | β = 96.005 |
c = 147.41 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 2020-06-25 | 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) | 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 | 1.85 | 50 | 99.2 | 0.075 | 0.085 | 0.998 | 14.7 | 4.668 | 154253 | 27.862 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.85 | 1.9 | 98.8 | 0.589 | 0.665 | 0.856 | 3.17 | 4.681 |
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 6XNQ | 1.85 | 48.87 | 1.35 | 154171 | 2025 | 99.16 | 0.1571 | 0.1567 | 0.1901 | 0 | 24 |
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 | 13.8536 |
f_angle_d | 0.9271 |
f_chiral_restr | 0.0608 |
f_bond_d | 0.0087 |
f_plane_restr | 0.0075 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11971 |
Nucleic Acid Atoms | |
Solvent Atoms | 1590 |
Heterogen Atoms | 260 |
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 |