D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with glycyl-3'-aminoadenosine at 2.10 Angstrom resolution
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3KNF | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 28% PEG 3350, 0.4M sodium chloride, 0.1M HEPES, pH 7.5 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.2 | 44.2 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 57.156 | α = 90 |
| b = 86.439 | β = 96.39 |
| c = 138.163 | 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 | 93 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2011-05-09 | 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 | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 2.1 | 25 | 96.5 | 0.112 | 14.7 | 4.9 | 75606 | ||||||||||||
| 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 | 2.1 | 2.18 | 0.876 | ||||||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3KNF | 2.1 | 25 | 71448 | 3690 | 96.15 | 0.22251 | 0.2201 | 0.22 | 0.26963 | 0.27 | RANDOM | 59.333 | ||||
| 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] | |
| 0.34 | -2.31 | 0.68 | -0.5 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 42.688 |
| r_dihedral_angle_3_deg | 16.107 |
| r_dihedral_angle_4_deg | 12.279 |
| r_long_range_B_refined | 7.23 |
| r_long_range_B_other | 7.221 |
| r_dihedral_angle_1_deg | 6.27 |
| r_scangle_other | 4.966 |
| r_mcangle_it | 4.429 |
| r_mcangle_other | 4.429 |
| r_scbond_it | 3.067 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 10044 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 179 |
| Heterogen Atoms | 184 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-2000 | data processing |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
