2QVN
Crystal structure of adenosine deaminase from Plasmodium vivax in complex with guanosine
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | 27.3% PEG 20000, 0.1 M CHES pH 9.5, 0.1 M Sodium phosphate monobasic, 5 mM Guanosine, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.08 | 60.07 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 144.548 | α = 90 |
| b = 146.922 | β = 90 |
| c = 50.453 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 2 2 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 | MARMOSAIC 325 mm CCD | mirrors | 2007-04-18 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.91837 | 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 | 2.19 | 40 | 99.6 | 0.146 | 5.6 | 6.6 | 27968 | 27968 | 30.2 | ||||||||||
| 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 | 2.19 | 2.28 | 97.1 | 0.678 | 1.7 | 5 | 2662 | ||||||||||||
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 | FOURIER SYNTHESIS | THROUGHOUT | PDB entry 2PGF | 2.19 | 35 | 27942 | 27942 | 1404 | 98.94 | 0.175 | 0.175 | 0.172 | 0.232 | RANDOM | 29.408 | ||||
| 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] | |
| 1.8 | -2.19 | 0.39 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.164 |
| r_dihedral_angle_4_deg | 20.21 |
| r_dihedral_angle_3_deg | 12.769 |
| r_scangle_it | 5.854 |
| r_dihedral_angle_1_deg | 5.344 |
| r_scbond_it | 4.349 |
| r_mcangle_it | 2.686 |
| r_mcbond_it | 2.067 |
| r_angle_refined_deg | 1.043 |
| r_angle_other_deg | 0.825 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2923 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 129 |
| Heterogen Atoms | 33 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| Blu-Ice | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| REFMAC | phasing |
