7K46
Crystal Structure of a putative aspartate carbamoyltransferase Leishmania major Friedlin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 287 | Microlytic MCSG1 screen, condition G7: 25% (w/V) PEG 3350, 100mM Tris base / HCl pH 8.5: LemaA.01332.a.AE1.PS38633 (originally labelled as MyavA.00358.f.AE1.PS38633) at 13.16mg/ml; tray 315258 G7; cryo: 20% EG in 2 steps; puck: ddy3-5. For phasing a crystal from the same tray, condition D4 (200mM sodium thiocyanate, 20% (w/V) PEG 3350) was soaked for 15 sec in a mix of 90% reservoir and 10% 2.5M NaI in EG, followed by a 15sec soak in a mix of 80% reservoir and 20% 2.5m NaI in EG: tray 315258 d4: puck ddy3-3 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.91 | 57.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 136.24 | α = 90 |
b = 136.24 | β = 90 |
c = 136.24 | γ = 90 |
Symmetry | |
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Space Group | I 2 3 |
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 | RIGAKU SATURN 944+ | 2018-08-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
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 | 1.9 | 50 | 100 | 0.059 | 0.061 | 1 | 32.55 | 15.975 | 33187 | 30.123 |
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 | 1.9 | 1.95 | 100 | 0.563 | 0.595 | 0.933 | 4.21 | 9.661 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | FREE R-VALUE | 1.9 | 48.17 | 1.34 | 33178 | 1954 | 99.96 | 0.1538 | 0.1523 | 0.1758 | 0 | 26.42 |
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 | 11.6174 |
f_angle_d | 0.7942 |
f_chiral_restr | 0.0529 |
f_plane_restr | 0.0074 |
f_bond_d | 0.0062 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2314 |
Nucleic Acid Atoms | |
Solvent Atoms | 421 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |
PARROT | phasing |
ARP/wARP | model building |
CRANK2 | phasing |
Coot | model building |