8I78
Meso-Diaminopimelate dehydrogenase
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3WBB | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 293.15 | 2M ammonium sulfate, 0.1M Sodium acetate trihydrate, pH 4.5 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.11 | 70.09 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 211.91 | α = 90 |
| b = 211.91 | β = 90 |
| c = 245.76 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | H 3 2 |
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 | Bruker PHOTON II | multilayer | 2021-06-25 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SEALED TUBE | BRUKER D8 QUEST | 1.54178 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.64 | 47.48 | 99.97 | 0.995 | 14.9 | 5.13 | 58941 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.64 | 2.71 | 0.689 | ||||||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.64 | 47.52 | 58941 | 3204 | 99.97 | 0.18491 | 0.18332 | 0.21409 | RANDOM | 37.672 | |||||||
| 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] | |
| -0.73 | -0.36 | -0.73 | 2.35 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.007 |
| r_dihedral_angle_4_deg | 19.029 |
| r_dihedral_angle_3_deg | 15.692 |
| r_long_range_B_refined | 8.079 |
| r_long_range_B_other | 8.078 |
| r_dihedral_angle_1_deg | 6.992 |
| r_scangle_other | 5.924 |
| r_mcangle_it | 4.492 |
| r_mcangle_other | 4.492 |
| r_scbond_it | 3.737 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8980 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 457 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
