2ABS
Crystal structure of T. gondii adenosine kinase complexed with AMP-PCP
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.1 | 295 | PEG 4000, ammonium acetate, magnesium chloride, sodium citrate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.1 | 41.2 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 60.051 | α = 90 |
| b = 67.923 | β = 90 |
| c = 83.192 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
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 | ADSC QUANTUM 315 | 2004-10-01 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 8-BM | 0.9777 | APS | 8-BM |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.1 | 50 | 93.7 | 0.062 | 13.6 | 3.1 | 129879 | 129879 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1.1 | 1.14 | 71.9 | 0.274 | 2.8 | 1.9 | 9849 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R | PDB entry 1LIO | 1.1 | 10 | 122947 | 122947 | 6466 | 89.1 | 0.1369 | 0.1369 | 0.1353 | 0.1665 | RANDOM | |||||
| 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] | |
| Coordinate Error | ||
|---|---|---|
| Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
| 76 | 2258.7 | 2967.97 |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| s_approx_iso_adps | 0.101 |
| s_non_zero_chiral_vol | 0.086 |
| s_zero_chiral_vol | 0.081 |
| s_anti_bump_dis_restr | 0.051 |
| s_similar_adp_cmpnt | 0.051 |
| s_angle_d | 0.032 |
| s_from_restr_planes | 0.0276 |
| s_bond_d | 0.014 |
| s_rigid_bond_adp_cmpnt | 0.005 |
| s_similar_dist | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2876 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 454 |
| Heterogen Atoms | 64 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SHELXL-97 | refinement |
| SCALEPACK | data scaling |
| CNS | refinement |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| CNS | phasing |
