3M4Q
Entamoeba histolytica asparaginyl-tRNA synthetase (AsnRS)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.6 | 298 | 0.2 ul 29 mg/ml protein in SGPP buffer mixed with 0.2 ul well soln. (100 mM HEPES pH 7.6, 25% PEG 3350, 200 mM MgCl2); cryoprotected by soaking ~1 min. in well soln supplemented with 10% PEG 200, vapor diffusion, sitting drop, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.54 | 51.6 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 102.047 | α = 90 |
| b = 102.047 | β = 90 |
| c = 205.015 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 21 2 |
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 325 mm CCD | 2008-04-28 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.979 | SSRL | BL11-1 |
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 | 3 | 50 | 99.8 | 0.121 | 9.2 | 13.9 | 22471 | 5 | 76 | ||||||||||
| 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) | |||||||||||
| 3 | 3.11 | 98.9 | 0.762 | 1.75 | 10.8 | 2174 | |||||||||||||
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 | 3m4p; A chain, protein only model | 3 | 45.8 | 22380 | 1144 | 99.66 | 0.222 | 0.22 | 0.267 | RANDOM | 87.156 | ||||||
| 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] | |
| 3.41 | 3.41 | -6.82 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.966 |
| r_dihedral_angle_4_deg | 17.304 |
| r_dihedral_angle_3_deg | 13.93 |
| r_dihedral_angle_1_deg | 5.494 |
| r_scangle_it | 2.376 |
| r_scbond_it | 1.475 |
| r_mcangle_it | 1.349 |
| r_angle_refined_deg | 0.958 |
| r_angle_other_deg | 0.765 |
| r_mcbond_it | 0.754 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6742 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| Blu-Ice | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
