Crystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH (E68A mutant)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 8.3 | 293 | 1.9 M ammonium sulfate, 0.1 M Tris pH 8.3, 10 mM TCEP, vapor diffusion, temperature 293K |
| 2 | VAPOR DIFFUSION | 8.3 | 293 | 1.9 M ammonium sulfate, 0.1 M Tris pH 8.3, 10 mM TCEP, soaking in 500 mM NaI during 30s, vapor diffusion, temperature 293K |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 116.92 | α = 90 |
| b = 116.92 | β = 90 |
| c = 55.58 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 63 |
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 | ADSC QUANTUM 210 | 2011-09-30 | M | SINGLE WAVELENGTH | ||||||
| 2 | 2 | x-ray | 100 | CCD | ADSC QUANTUM 210 | 2011-09-30 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.93340 | ESRF | ID14-1 |
| 2 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.93340 | ESRF | ID14-1 |
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 | 2.2 | 48.72 | 99.9 | 0.054 | 20.8 | 22194 | 22172 | -3 | -3 | 49.87 | |||||||||
| 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) | |||||||||||
| 1,2 | 2.2 | 2.32 | 99.4 | 0.839 | 2 | 5.6 | 17999 | ||||||||||||
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 | SIRAS | THROUGHOUT | 2.2 | 37.43 | 22157 | 1132 | 99.78 | 0.2142 | 0.2126 | 0.23 | 0.2446 | 0.26 | RANDOM | 59.5809 | |||||
| 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] | |
| 2.0839 | 2.0839 | -4.1678 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| t_other_torsion | 19.17 |
| t_omega_torsion | 2.33 |
| t_angle_deg | 0.99 |
| t_bond_d | 0.009 |
| t_dihedral_angle_d | |
| t_trig_c_planes | |
| t_gen_planes | |
| t_it | |
| t_chiral_improper_torsion | |
| t_ideal_dist_contact | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2606 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 58 |
| Heterogen Atoms | 15 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SHARP | phasing |
| BUSTER-TNT | refinement |
| PDB_EXTRACT | data extraction |
| ADSC | data collection |
| XDS | data reduction |
| XSCALE | data scaling |
| BUSTER | refinement |














