5NBK
NDM-1 metallo-beta-lactamase: a parsimonious interpretation of the diffraction data
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 298 | 24 % PEG 1500 AND 0.05 M TBG (SODIUM TARTRATE/BIS - TRIS/GLYCYLGLYCINE) PH 4 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.75 | 55.31 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 108.047 | α = 90 |
| b = 108.047 | β = 90 |
| c = 92.571 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 21 2 |
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-F | 2014-09-13 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SLS BEAMLINE X06DA | SLS | X06DA | |
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 | 2.6 | 46.66 | 100 | 999 | 9.2 | 17411 | |||||||||||||
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 | FREE R-VALUE | 2.6 | 46.66 | 16540 | 871 | 99.94 | 0.18298 | 0.18055 | 0.19 | 0.22928 | 0.23 | copied from 5a5z | 42.719 | ||||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
| 0.09 | 0.09 | -0.19 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.371 |
| r_dihedral_angle_4_deg | 20.329 |
| r_dihedral_angle_3_deg | 15.052 |
| r_dihedral_angle_1_deg | 6.626 |
| r_long_range_B_refined | 3.989 |
| r_long_range_B_other | 3.987 |
| r_scangle_other | 2.14 |
| r_mcangle_it | 1.68 |
| r_mcangle_other | 1.68 |
| r_angle_refined_deg | 1.504 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3441 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 109 |
| Heterogen Atoms | 61 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
