2OLC
Crystal structure of 5-methylthioribose kinase in complex with ADP-2Ho
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 22%(w/v) PEG2000MME, 0.1M TrisHCl pH 7.5 and 0.3M sodium acetate, vapor diffusion, hanging drop, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.57 | 52.14 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 215.2 | α = 90 |
| b = 83.6 | β = 90 |
| c = 51.6 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 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 QUANTUM 4r | mirrors | 2003-08-27 | M | SINGLE WAVELENGTH | |||||
| 2 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IV++ | osmic | 2004-09-01 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSLS BEAMLINE X8C | 1.5362 | NSLS | X8C |
| 2 | ROTATING ANODE | RIGAKU | 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 | 2 | 71.73 | 98.8 | 0.093 | 21.9 | 26.94 | 63253 | 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) | |||||||||||
| 1,2 | 2 | 2.07 | 97.5 | 0.434 | 9.2 | 26.57 | 6169 | ||||||||||||
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 | 2 | 107.83 | 63173 | 3148 | 98.79 | 0.215 | 0.214 | 0.25 | RANDOM | 27.565 | |||||||
| 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] | |
| -1.53 | -0.23 | 1.76 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.241 |
| r_dihedral_angle_4_deg | 15.694 |
| r_dihedral_angle_3_deg | 14.56 |
| r_dihedral_angle_1_deg | 5.723 |
| r_scangle_it | 2.27 |
| r_scbond_it | 1.558 |
| r_angle_refined_deg | 1.324 |
| r_mcangle_it | 0.841 |
| r_mcbond_it | 0.495 |
| r_nbtor_refined | 0.305 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5917 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 434 |
| Heterogen Atoms | 87 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| d*TREK | data scaling |
| SHELX | phasing |
| RESOLVE | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| CrystalClear | data collection |
| d*TREK | data reduction |
| SHELXDE | phasing |
