3PY6
Crystal Structure of a Beta-Lactamase-Like Protein from Brucella Melitensis bound to GMP
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8 | 290 | 15-18% PEG 3350, 200mM K/Na tartrate, 100mM BisTrisPropane pH 8.0, BrabA.11339.a.PW27637 at 18mg/ml supplemented with 1mM GMPPNP and 2mM MgCl2 at 18mg/ml, cryo: 21% PEG 3350, 15% EG, 165mM K/Na tartrate, 87mM BisTrisPropane pH 8.0, 1mM GMPPNP, 2mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.2 | 44.02 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 72.86 | α = 90 |
| b = 75.23 | β = 90 |
| c = 98.54 | 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 | RIGAKU SATURN 944+ | 2010-12-06 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 | ||
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 | 50 | 99.5 | 0.037 | 39.96 | 9.1 | 30143 | 29984 | -3 | 17.56 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 1.7 | 1.74 | 93.1 | 0.147 | 0.147 | 9.1 | 4.4 | 2221 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 3md7 | 1.7 | 36.43 | 30143 | 29910 | 1542 | 99.2 | 0.141 | 0.141 | 0.14 | 0.168 | RANDOM | 8.13 | ||||
| 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] | |
| -0.15 | -0.17 | 0.32 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.86 |
| r_dihedral_angle_4_deg | 15.196 |
| r_dihedral_angle_3_deg | 11.454 |
| r_dihedral_angle_1_deg | 6.165 |
| r_scangle_it | 3.172 |
| r_scbond_it | 1.98 |
| r_angle_refined_deg | 1.517 |
| r_mcangle_it | 1.215 |
| r_angle_other_deg | 0.936 |
| r_mcbond_it | 0.698 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2116 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 344 |
| Heterogen Atoms | 37 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| Structure | data collection |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
