X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | MRC plates with 1:1 ratio drops (enzyme:reservoir solution) and 100 ul reservoir using an Oryx-8 robot. Protein: 13.3 mg/ml in 20 mM MES pH 6.0. Reservoir: 20 mM L-Na-Glutamate, 20 mM DL-Alanine (racemic), 20 mM Glycine, 20 mM DL-Lysine HCl (racemic), 20 mM DL-Serine (racemic), 50 mM MES monohydrate pH 6.5, 50 mM imidazole pH 6.5. 20% (w/v) PEG 500 MME and 10% (w/v) PEG 20000. |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.42 | 64.03 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 84.599 | α = 90 |
| b = 84.635 | β = 90 |
| c = 127.319 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M-F | 2018-05-06 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 1.299 | ESRF | ID29 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | 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 | 2.08 | 100 | 99.6 | 0.152 | 0.998 | 12.93 | 14 | 57268 | -3 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 2.08 | 2.13 | 98.5 | 1.398 | 0.744 | 1.07 | 14.3 | ||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.08 | 42.35 | 52714 | 2641 | 99.53 | 0.2454 | 0.24417 | 0.2504 | 0.27087 | 0.275 | RANDOM | 43.444 | |||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
| 1.04 | 1.78 | -2.82 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.884 |
| r_dihedral_angle_3_deg | 13.254 |
| r_dihedral_angle_4_deg | 11.447 |
| r_long_range_B_other | 8.353 |
| r_long_range_B_refined | 8.352 |
| r_dihedral_angle_1_deg | 6.698 |
| r_scangle_other | 6.226 |
| r_mcangle_it | 4.833 |
| r_mcangle_other | 4.832 |
| r_scbond_it | 4.237 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4569 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 549 |
| Heterogen Atoms | 386 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MxCuBE | data collection |
| XDS | data reduction |
| XSCALE | data scaling |
| PHENIX | phasing |
| AutoSol | phasing |
| PHASER | phasing |
| Coot | model building |
