2DYU
Helicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine catalytic triad
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 0.1M sodium cacodylate, 0.15M potassium thiocyanate, 20% polyethylene glycol 550 MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.02 | 39.04 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 147.215 | α = 90 |
| b = 147.215 | β = 90 |
| c = 72.273 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | H 3 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 113 | CCD | ADSC QUANTUM 4 | 2004-07-11 | M | SINGLE WAVELENGTH | ||||||
| 2 | 1 | x-ray | 113 | CCD | ADSC QUANTUM 4 | 2004-07-11 | M | |||||||
| 1,2 | 1 | |||||||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL12B2 | 0.9800 | SPring-8 | BL12B2 |
| 2 | SYNCHROTRON | SPRING-8 BEAMLINE BL12B2 | 0.9791 | SPring-8 | BL12B2 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.75 | 30 | 99.7 | 3.2 | 58786 | 58786 | |||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1,2 | 1.75 | 1.81 | 100 | ||||||||||||||||
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 | 1.75 | 30 | 55500 | 2960 | 98.95 | 0.1764 | 0.17433 | 0.21515 | RANDOM | 23.57 | |||||||
| 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] | |
| 0.04 | 0.02 | 0.04 | -0.06 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.514 |
| r_dihedral_angle_4_deg | 16.181 |
| r_dihedral_angle_3_deg | 13.278 |
| r_dihedral_angle_1_deg | 5.574 |
| r_scangle_it | 2.02 |
| r_scbond_it | 1.257 |
| r_mcangle_it | 1.068 |
| r_angle_refined_deg | 1.037 |
| r_mcbond_it | 0.611 |
| r_nbtor_refined | 0.321 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5098 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 713 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| SOLVE | phasing |
