Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8 | 295 | 0.2 M Ammonium chloride, 0.1 M Hepes pH 8, 20% PEG 6000 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.74 | 55.03 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 345.954 | α = 90 |
| b = 42.549 | β = 93.07 |
| c = 79.318 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 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 PILATUS 2M | 2013-03-11 | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.916 | Diamond | I04-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.8 | 47.8 | 98.3 | 7.8 | 3.4 | 47327 | |||||||||||||
| 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 | 2.8 | 2.95 | 98.3 | 1.9 | 3.4 | ||||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | THROUGHOUT | 2.8 | 47.8 | 27113 | 1457 | 97.9 | 0.276 | 0.273 | 0.27 | 0.334 | 0.33 | RANDOM | 43.86 | ||||||
| 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] | |
| -0.1 | 1.22 | -0.03 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.416 |
| r_dihedral_angle_3_deg | 13.447 |
| r_dihedral_angle_4_deg | 8.276 |
| r_dihedral_angle_1_deg | 4.794 |
| r_long_range_B_refined | 3.649 |
| r_long_range_B_other | 3.649 |
| r_mcangle_it | 1.702 |
| r_mcangle_other | 1.702 |
| r_scangle_other | 1.312 |
| r_mcbond_it | 0.952 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 7065 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 111 |
| Heterogen Atoms | 31 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
