6B4A
Crystal structure of the C-Terminal Domain of Doublecortin (TgDCX) from Toxoplasma gondii ME49
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 289 | Rigaku Reagents PACT screen, optimized condition e6: 24.09% (w/v) PEG 3350, 50 mM sodium formate: TogoA.17199.a.B3.PW38274 at 15 mg/mL: cryo: 20% EG: tray 293956a11: puck utu4-1. For phasing, a crystal from Rigaku Reagents PACT screen condition e6 (18% (w/v) PEG 3350, 200 mM sodium formate) was soaked in reservoir plus 20% 2.5 M NaI in ethylene glycol and vitrified. Anomalous data was collected at the home source. Tray 292844e6: puck hly3-2. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.94 | 36.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.86 | α = 90 |
b = 53.23 | β = 90 |
c = 96.38 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 100 | CCD | RIGAKU SATURN 944+ | 2017-08-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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 | 2 | 35.725 | 99.8 | 0.059 | 0.064 | 0.999 | 17.97 | 6.112 | 13417 | -3 | 30.77 |
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 | 2 | 2.05 | 99.8 | 0.557 | 0.645 | 0.842 | 2.65 | 3.916 |
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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SAD | FREE R-VALUE | 2 | 35.725 | 1.35 | 13372 | 1423 | 99.82 | 0.1935 | 0.1857 | 0.2607 | 45.6687 |
Temperature Factor Modeling | ||||||
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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 | 10.252 |
f_angle_d | 0.784 |
f_chiral_restr | 0.054 |
f_bond_d | 0.007 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1463 |
Nucleic Acid Atoms | |
Solvent Atoms | 104 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
ARP | model building |