3GN1
Structure of Pteridine Reductase 1 (PTR1) from TRYPANOSOMA BRUCEI in ternary complex with cofactor (NADP+) and inhibitor (DDD00067116)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 4.5 | 2-3M SODIUM ACETATE, 10-100MM SODIUM CITRATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.05 | 39.89 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 74.641 | ¦Á = 90 |
| b = 90.408 | ¦Â = 115.73 |
| c = 82.638 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 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 | IMAGE PLATE | RIGAKU RAXIS IV | M | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | |||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 30.66 | 94.8 | 0.051 | 0.051 | 9.3 | 5.4 | 63246 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 2 | 2.11 | 89.9 | 0.136 | 0.136 | 5.1 | 5.3 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2 | 30.66 | 63194 | 3203 | 94.5 | 0.158 | 0.155 | 0.216 | 12.03 | |||||||||
| 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] | |
| -1.03 | -0.81 | 1.52 | -1.19 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.715 |
| r_dihedral_angle_4_deg | 19.617 |
| r_dihedral_angle_3_deg | 14.362 |
| r_dihedral_angle_1_deg | 6.049 |
| r_scangle_it | 5.911 |
| r_scbond_it | 4.744 |
| r_mcangle_it | 3.15 |
| r_mcbond_it | 2.332 |
| r_angle_refined_deg | 1.474 |
| r_nbtor_refined | 0.296 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 7417 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 896 |
| Heterogen Atoms | 230 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MOLREP | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
