5EIN
Crystal structure of C148A mutant of LysY from Thermus thermophilus in complex with NADP+ and LysW-gamma-aminoadipic acid
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | PEG 3350, magnesium formate, NADP+, HEPES-NaOH |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.06 | 40.31 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 83.54 | α = 90 |
| b = 83.54 | β = 90 |
| c = 167.781 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 32 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 | 100 | CCD | ADSC QUANTUM 270 | 2014-02-08 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NE3A | 1.0 | Photon Factory | AR-NE3A |
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 | 1.7 | 50 | 98.9 | 38.1 | 5.5 | 75384 | |||||||||||||
| 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 | 1.7 | 1.73 | 100 | 0.441 | 4.2 | 5.2 | |||||||||||||
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 | 5EIO | 1.7 | 44.25 | 70757 | 3761 | 98.9 | 0.173 | 0.171 | 0.21 | RANDOM | 29.66 | ||||||
| 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 |
| r_dihedral_angle_2_deg | 33.742 |
| r_dihedral_angle_4_deg | 17.352 |
| r_dihedral_angle_3_deg | 14.45 |
| r_dihedral_angle_1_deg | 6.17 |
| r_long_range_B_refined | 5.392 |
| r_long_range_B_other | 5.392 |
| r_scangle_other | 3.104 |
| r_mcangle_it | 2.665 |
| r_mcangle_other | 2.665 |
| r_scbond_it | 1.97 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5779 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 553 |
| Heterogen Atoms | 166 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Coot | model building |
| HKL-2000 | data scaling |
| HKL-2000 | data collection |
| PHASER | phasing |
