1SNF
MYCOBACTERIUM TUBERCULOSIS DUTPASE COMPLEXED WITH MAGNESIUM AND DEOXYURIDINE 5'-MONOPHOSPHATE
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1MQ7 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8 | 298 | PEG 3350, magnesium nitrate, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.52 | 50.74 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 58.228 | α = 90 |
| b = 77.496 | β = 90 |
| c = 93.949 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 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 | ADSC QUANTUM 4 | mirrors | 2002-10-25 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSLS BEAMLINE X8C | 1.10 | NSLS | X8C |
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 | 1.85 | 80 | 97.9 | 0.07 | 14.8 | 3.5 | 36211 | 36211 | 19.3 | ||||||||||
| 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) | |||||||||||
| 1 | 1.85 | 1.92 | 98.7 | 0.462 | 2.9 | 3 | 3579 | ||||||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1MQ7 | 1.85 | 41.89 | 31243 | 31243 | 3485 | 95.99 | 0.173 | 0.17293 | 0.16931 | 0.20462 | RANDOM | 18.363 | ||||
| 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] | |
| -0.3 | -1.88 | 2.18 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_1_deg | 6.392 |
| r_scangle_it | 4.387 |
| r_angle_refined_deg | 2.716 |
| r_scbond_it | 2.62 |
| r_mcangle_it | 1.621 |
| r_angle_other_deg | 1.373 |
| r_mcbond_it | 0.989 |
| r_symmetry_vdw_other | 0.352 |
| r_nbd_other | 0.248 |
| r_symmetry_vdw_refined | 0.223 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2917 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 246 |
| Heterogen Atoms | 91 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| EPMR | phasing |
