7Y5P
Crystal structure of CmnC in complex with L-arginine and alpha-KG
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | 0.2M Ammonium acetate, 0.1M Na citrate tribasic dihydrate pH 5.5, 24% v/v Polyethylene glycol 400 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.78 | 55.72 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 92.998 | α = 90 |
| b = 127.292 | β = 90 |
| c = 139.019 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 2 2 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 | CCD | ADSC QUANTUM 315r | 2022-06-02 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSRRC BEAMLINE BL15A1 | 0.9732 | NSRRC | BL15A1 |
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 | 1.7 | 30 | 99.7 | 0.055 | 27.56 | 5.5 | 90120 | ||||||||||||
| 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 | 1.76 | 100 | 0.604 | 2.42 | ||||||||||||||
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 | 7VGL | 1.7 | 26.28 | 82573 | 4384 | 95.94 | 0.1788 | 0.1775 | 0.2036 | RANDOM | 17.297 | ||||||
| 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] | |
| -0.13 | -0.04 | 0.17 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 27.91 |
| r_dihedral_angle_4_deg | 15.444 |
| r_dihedral_angle_3_deg | 12.536 |
| r_dihedral_angle_1_deg | 6.935 |
| r_angle_other_deg | 1.32 |
| r_angle_refined_deg | 1.291 |
| r_chiral_restr | 0.059 |
| r_bond_refined_d | 0.006 |
| r_gen_planes_refined | 0.005 |
| r_bond_other_d | 0.001 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5222 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 503 |
| Heterogen Atoms | 33 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| MOLREP | phasing |
