4H4J
Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.15 A resolution
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 277 | 30.0% polyethylene glycol 1500, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2 | 38.58 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 46.349 | α = 90 |
| b = 63.713 | β = 90 |
| c = 72.962 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 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 | PIXEL | DECTRIS PILATUS 6M | Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator | 2012-07-16 | M | SAD | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | SSRL | BL12-2 | |
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 | 1.15 | 28.666 | 92.1 | 0.067 | 12.95 | 71198 | -3 | 11.453 | |||||||||||
| 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 | 1.15 | 1.19 | 60.2 | 0.883 | 1.84 | 13.15 | |||||||||||||
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 | SAD | THROUGHOUT | 1.15 | 28.666 | 71147 | 3572 | 91.92 | 0.1323 | 0.1306 | 0.164 | RANDOM | 18.3283 | |||||||
| 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 | -0.1 | |||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.773 |
| r_dihedral_angle_4_deg | 18.843 |
| r_dihedral_angle_3_deg | 12.434 |
| r_sphericity_free | 11.227 |
| r_scangle_it | 6.496 |
| r_sphericity_bonded | 6.305 |
| r_dihedral_angle_1_deg | 6.07 |
| r_scbond_it | 4.721 |
| r_mcangle_it | 3.871 |
| r_mcbond_it | 2.746 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1840 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 431 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MolProbity | model building |
| PDB_EXTRACT | data extraction |
| SHELX | phasing |
| SHARP | phasing |
| XSCALE | data scaling |
| REFMAC | refinement |
| XDS | data reduction |
| SHELXD | phasing |
