1XJF
Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP complex
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1RLR | PDB entry 1RLR |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 293 | PEG8000, sodium acetate, sodium chloride, dithiotreithol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.55 | 55 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 116.3 | ¦Á = 90 |
| b = 123.76 | ¦Â = 103.82 |
| c = 107.03 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 1 |
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 | MARRESEARCH | 2002-02-17 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | MAX II BEAMLINE I711 | 1.076 | MAX II | I711 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.4 | 25 | 99.3 | 0.063 | 12.1 | 3.75 | 57137 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 2.4 | 2.6 | 99.5 | 0.388 | 3.2 | |||||||||||||||
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 | PDB entry 1RLR | 2.4 | 22.88 | 54368 | 2935 | 99.75 | 0.21105 | 0.20836 | 0.26026 | RANDOM | 46.783 | ||||||
| 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] | |
| -0.11 | -0.06 | 0.06 | 0.02 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.996 |
| r_dihedral_angle_4_deg | 22.55 |
| r_dihedral_angle_3_deg | 18.675 |
| r_dihedral_angle_1_deg | 6.871 |
| r_scangle_it | 3.441 |
| r_scbond_it | 2.115 |
| r_angle_refined_deg | 1.651 |
| r_mcangle_it | 1.57 |
| r_mcbond_it | 0.883 |
| r_metal_ion_refined | 0.572 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 9878 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 254 |
| Heterogen Atoms | 62 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MAR345 | data collection |
| CCP4 | data scaling |
| CNS | phasing |
