Crystal Structure of succinyl-diaminopimelate desuccinylase from Neisseria meningitidis MC58 in complex with the Inhibitor Captopril
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 289 | 0.2M Ammonium acetate 0.1M Tris8.5; 25% w/vPolyethylene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.95 | 58.28 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 116.921 | α = 90 |
| b = 151.487 | β = 90 |
| c = 55.098 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 2 2 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 | CCD | ADSC QUANTUM 315r | mirrors | 2013-12-12 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.9794 | APS | 19-ID |
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 | 1.78 | 27.6 | 97.7 | 0.065 | 18 | 3.9 | 46112 | 46112 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1 | 1.78 | 1.81 | 99.3 | ||||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | 1.78 | 27.55 | 41541 | 39438 | 2103 | 87.97 | 0.16381 | 0.16192 | 0.17 | 0.19622 | 0.21 | RANDOM | 25.307 | ||||
| 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] | |
| -0.69 | 1.08 | -0.39 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.584 |
| r_dihedral_angle_4_deg | 17.848 |
| r_dihedral_angle_3_deg | 12.552 |
| r_dihedral_angle_1_deg | 6.268 |
| r_angle_refined_deg | 1.9 |
| r_angle_other_deg | 0.9 |
| r_chiral_restr | 0.128 |
| r_bond_refined_d | 0.021 |
| r_gen_planes_refined | 0.01 |
| r_bond_other_d | 0.001 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2866 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 344 |
| Heterogen Atoms | 21 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SBC-Collect | data collection |
| MOLREP | phasing |
| CCP4 | model building |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| CCP4 | phasing |
