5NS1
Cys-Gly dipeptidase GliJ in complex with Ni2+
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6 | 293 | 0.1 M MES pH 6.0, 5% isopropanol |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.4 | 63.81 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 99.35 | α = 90 |
| b = 99.35 | β = 90 |
| c = 107.37 | 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 | PIXEL | DECTRIS EIGER X 16M | 2017-04-08 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.48432 | SLS | X06SA |
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 | 2.4 | 45 | 99.9 | 0.062 | 12 | 4.3 | 46316 | ||||||||||||
| 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 | 2.4 | 2.5 | 99.9 | 0.598 | 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 | 5LX0 | 2.4 | 15 | 23080 | 1214 | 99.44 | 0.18508 | 0.18426 | 0.20052 | RANDOM | 69.831 | ||||||
| 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] | |
| 0.56 | 0.28 | 0.56 | -1.82 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.971 |
| r_sphericity_free | 29.146 |
| r_dihedral_angle_3_deg | 12.945 |
| r_dihedral_angle_4_deg | 12.796 |
| r_sphericity_bonded | 6.094 |
| r_dihedral_angle_1_deg | 5.252 |
| r_long_range_B_refined | 2.044 |
| r_long_range_B_other | 2.027 |
| r_scbond_it | 1.545 |
| r_scbond_other | 1.544 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3007 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 76 |
| Heterogen Atoms | 3 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| REFMAC | phasing |
