4PU9
E. coli GyrB 43-kDa N-terminal fragment in complex with ADP-BeF3
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293.15 | 0.2M NaF, 0.1M Bis-Tris propane pH 6.5 and 20%(w/v) PEG3350, vapor diffusion, sitting drop, temperature 293.15K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.05 | 59.32 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 88.083 | α = 90 |
| b = 143.245 | β = 90 |
| c = 79.895 | 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 | PIXEL | DECTRIS PILATUS 2M | 2013-11-20 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SLS BEAMLINE X06DA | 0.97932 | SLS | X06DA |
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 | 2.4 | 79.92 | 99.7 | 0.076 | 16.6 | 6.9 | 20138 | 20138 | -3 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 2.4 | 2.49 | 99.6 | 0.385 | 0.154 | 4.9 | 7.1 | 2086 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 | 1EI1 | 2.4 | 44.08 | -3 | 19991 | 19991 | 1022 | 99.2 | 0.2217 | 0.2217 | 0.2189 | 0.2733 | RANDOM | 41.852 | |||
| 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] | |
| -4.51 | 6.71 | -2.2 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 38.715 |
| r_dihedral_angle_3_deg | 18.73 |
| r_dihedral_angle_4_deg | 18.474 |
| r_dihedral_angle_1_deg | 6.758 |
| r_angle_refined_deg | 1.961 |
| r_angle_other_deg | 0.901 |
| r_chiral_restr | 0.106 |
| r_bond_refined_d | 0.016 |
| r_gen_planes_refined | 0.008 |
| r_bond_other_d | 0.001 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2890 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 48 |
| Heterogen Atoms | 32 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| Aimless | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
