4ZLV
Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with the Schiff base between PLP and Lys286
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 4NGO |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 294 | 0.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.11 | 41.76 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 56.481 | α = 100.45 |
b = 61.459 | β = 92.39 |
c = 63.435 | γ = 108.32 |
Symmetry | |
---|---|
Space Group | P 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 | CCD | MARMOSAIC 300 mm CCD | 2015-03-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 0.97889 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.8 | 30 | 96 | 0.03 | 22.1 | 1.8 | 70729 | 70729 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.8 | 1.83 | 87.4 | 0.46 | 1.5 | 1.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 4NGO | 1.8 | 30 | 67239 | 3490 | 95.69 | 0.16408 | 0.16191 | 0.20591 | RANDOM | 35.798 |
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] | |
0.01 | -2.64 | -0.62 | 1.29 | -0.53 | 0.53 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.109 |
r_dihedral_angle_4_deg | 17.303 |
r_dihedral_angle_3_deg | 13.143 |
r_dihedral_angle_1_deg | 6.321 |
r_long_range_B_refined | 5.727 |
r_long_range_B_other | 5.675 |
r_scangle_other | 1.716 |
r_angle_refined_deg | 1.628 |
r_mcangle_it | 1.225 |
r_mcangle_other | 1.225 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6533 |
Nucleic Acid Atoms | |
Solvent Atoms | 503 |
Heterogen Atoms | 67 |
Software
Software | |
---|---|
Software Name | Purpose |
BLU-MAX | data collection |
HKL-3000 | phasing |
HKL-3000 | data scaling |
PHASER | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |