An aldehyde-containing intermediate of SufS in complex with (2R,3R)-3-ethoxycarbonylaziridine-2-carboxylic acid
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6KFY | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 0.1 M Tris-HCl, 50 mM Lithium sulfate, 50% (v/v) PEG200 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.42 | 64 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 92.7 | α = 90 |
| b = 92.7 | β = 90 |
| c = 128.32 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 31 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 PILATUS3 6M | 2021-11-13 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1 | Photon Factory | BL-5A |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.2 | 50 | 100 | 0.065 | 0.068 | 1 | 23.67 | 10.1 | 32955 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 2.2 | 2.3 | 0.832 | 0.877 | 0.828 | ||||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6KFY | 2.2 | 46.35 | 31304 | 1648 | 99.98 | 0.17602 | 0.1741 | 0.1742 | 0.21223 | 0.2124 | RANDOM | 49.817 | ||||
| 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] | |
| -0.09 | -0.04 | -0.09 | 0.29 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 14.06 |
| r_long_range_B_refined | 8.675 |
| r_dihedral_angle_2_deg | 7.636 |
| r_dihedral_angle_1_deg | 6.67 |
| r_scbond_it | 5.173 |
| r_mcangle_it | 4.312 |
| r_mcbond_it | 3.35 |
| r_angle_refined_deg | 1.907 |
| r_chiral_restr | 0.12 |
| r_bond_refined_d | 0.009 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3173 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 164 |
| Heterogen Atoms | 29 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XSCALE | data scaling |
| XDS | data reduction |
| PHASER | phasing |
