5M49
Alpha-amino epsilon-caprolactam racemase in complex with PLP and D/L alpha amino epsilon-caprolactam (internal aldimine)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 290 | 0.2 M MgCl2, 25 % PEG 3350, 0.1 mM HEPES (pH 7.0). |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.98 | 37.91 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 87.696 | α = 90 |
| b = 77.679 | β = 112.68 |
| c = 57.602 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 120 | PIXEL | DECTRIS PILATUS 6M-F | 2015-04-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.97949 | Diamond | I04 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.51 | 45.03 | 99.6 | 0.025 | 33.9 | 4.1 | 55609 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.51 | 1.54 | 0.057 | 2734 | |||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2ZUK | 1.51 | 56.04 | 52841 | 2767 | 99.57 | 0.1629 | 0.1612 | 0.19508 | RANDOM | 15.805 | ||||||
| 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] | |
| -0.07 | -0.18 | 0.49 | -0.2 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.489 |
| r_dihedral_angle_4_deg | 22.889 |
| r_dihedral_angle_3_deg | 12.611 |
| r_dihedral_angle_1_deg | 6.284 |
| r_long_range_B_refined | 4.845 |
| r_long_range_B_other | 4.844 |
| r_scangle_other | 3.754 |
| r_scbond_it | 2.62 |
| r_scbond_other | 2.619 |
| r_angle_refined_deg | 2.538 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3074 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 274 |
| Heterogen Atoms | 33 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
