5HYY
Crystal structure of N-terminal amidase
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 293 | 0.2M Ammonium acetate, 0.1M TriNa citrate dihydrate pH5.6, 30%(w/v) PEG 4000 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.65 | 53.55 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 94.886 | α = 90 |
| b = 94.886 | β = 90 |
| c = 61.259 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 42 |
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 315r | 2012-06-22 | M | MAD | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PAL/PLS BEAMLINE 5C (4A) | 0.97951 | PAL/PLS | 5C (4A) |
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 | 2.3 | 37.509 | 99.9 | 42.4 | 8.1 | 23487 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | NONE | 2.323 | 37.509 | 1.34 | 23486 | 2004 | 99.06 | 0.1998 | 0.1957 | 0.2427 | |||||||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 11.417 |
| f_angle_d | 0.806 |
| f_chiral_restr | 0.03 |
| f_bond_d | 0.004 |
| f_plane_restr | 0.004 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3318 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 103 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
