2BZG
Crystal structure of thiopurine S-methyltransferase.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | PROTEIN WAS CRYSTALLIZED IN THE PRESENCE OF 6-MERCAPTOPURINE-9-B, D-RIBOFURANOSIDE (PROTEIN: 6-MP-RIBOFURANOSIDE= 1:10) USING THE HANGING DROP VAPOR DIFFUSION METHOD AT 20C BY MIXING 1.5 UL OF THE PROTEIN SOLUTION WITH 1.5 UL OF THE RESERVOIR SOLUTION CONTAINING 24% PEG3350, 0.2 M KCNS, 0.1 M BISTRIS PROPANE, PH 7.0. |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.4 | 48 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 85.486 | α = 90 |
| b = 85.486 | β = 90 |
| c = 69.362 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 42 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 | ADSC CCD | 2005-07-14 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 17-ID | APS | 17-ID | |
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 | 1.58 | 36.39 | 99 | 0.07 | 11.8 | 7.09 | 67746 | 5 | |||||||||||
| 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 | 1.58 | 1.64 | 92.9 | 0.27 | 4.1 | 4.24 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.58 | 60.41 | 33511 | 1756 | 98.5 | 0.214 | 0.213 | 0.249 | RANDOM | 18.45 | |||||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.474 |
| r_dihedral_angle_4_deg | 17.856 |
| r_dihedral_angle_3_deg | 13.146 |
| r_dihedral_angle_1_deg | 6.026 |
| r_angle_refined_deg | 1.384 |
| r_symmetry_hbond_refined | 0.366 |
| r_nbtor_refined | 0.309 |
| r_nbd_refined | 0.202 |
| r_symmetry_vdw_refined | 0.186 |
| r_xyhbond_nbd_refined | 0.101 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1858 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 231 |
| Heterogen Atoms | 45 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| d*TREK | data reduction |
| d*TREK | data scaling |
