4XLL
Toxoplasma gondii DJ-1, oxidized
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 291 | 1:1 5mg/mL protein in 10 mM HEPES 7.0, 100 mM NaCl, 10 mM DTT mixed with reservoir: 1.5 M ammonium citrate tribasic |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.01 | 38.9 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 38.777 | α = 90 |
b = 55.181 | β = 93.92 |
c = 75.247 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2013-05-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.979450 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2.08 | 38.6929 | 97.2 | 0.092 | 0.099 | 16.96 | 6.84 | 18638 | -3 | 25.499 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.08 | 2.14 | 90.3 | 0.338 | 0.368 | 5.25 | 6.3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | THROUGHOUT | 2.08 | 38.69 | 18630 | 1811 | 93.42 | 0.1736 | 0.1686 | 0.2188 | RANDOM | 22.525 |
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] | |
4.6 | 1.35 | -2.93 | -1.84 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.919 |
r_dihedral_angle_3_deg | 13.265 |
r_dihedral_angle_4_deg | 12.574 |
r_dihedral_angle_1_deg | 6.636 |
r_mcangle_it | 2.003 |
r_angle_refined_deg | 1.668 |
r_mcbond_it | 1.269 |
r_mcbond_other | 1.264 |
r_angle_other_deg | 1.032 |
r_chiral_restr | 0.094 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2742 |
Nucleic Acid Atoms | |
Solvent Atoms | 245 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |