1YVM
E. coli Methionine Aminopeptidase in complex with thiabendazole
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2MAT | PDB ENTRY 2MAT |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.1 | 293 | PEG 4000, cobalt chloride, hepes, methionine, sodium chloride, potassium chloride, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.99 | 38.11 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 38.91 | α = 90 |
| b = 66.13 | β = 111.25 |
| c = 48.53 | γ = 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 | 103 | IMAGE PLATE | RIGAKU RAXIS IV++ | OSMIC mirrors | 2004-10-21 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RU300 | 1.5418 | ||
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 | 1.6 | 30 | 98.2 | 0.086 | 14.8 | 3.4 | 29881 | 29881 | |||||||||||
| 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) | |||||||||||
| 1.6 | 1.63 | 75.8 | 0.418 | 2.9 | 2.5 | ||||||||||||||
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 | FREE R | PDB ENTRY 2MAT | 1.6 | 30 | 28751 | 28751 | 1414 | 94.6 | 0.1699 | 0.1699 | 0.168 | 0.2331 | RANDOM | |||||
| 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] | |
| Coordinate Error | ||
|---|---|---|
| Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
| 4 | 2044 | 2321 |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| s_from_restr_planes | 0.389 |
| s_similar_adp_cmpnt | 0.069 |
| s_non_zero_chiral_vol | 0.049 |
| s_zero_chiral_vol | 0.047 |
| s_angle_d | 0.027 |
| s_anti_bump_dis_restr | 0.016 |
| s_bond_d | 0.009 |
| s_similar_dist | |
| s_rigid_bond_adp_cmpnt | |
| s_approx_iso_adps | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2056 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 270 |
| Heterogen Atoms | 19 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SHELX | model building |
| SHELXL-97 | refinement |
| CrystalClear | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
| CNS | phasing |
