2HKV
CRYSTAL STRUCTURE OF A PUTATIVE MEMBER OF THE DINB FAMILY (EXIG_1237) FROM EXIGUOBACTERIUM SIBIRICUM 255-15 AT 1.70 A RESOLUTION
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 277 | 20.0% PEG-3350, 0.2M MgSO4,, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K | |
| 2 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 293 | 20.0% PEG-3350, 0.2M MgSO4,, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K | |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 45.02 | α = 90 |
| b = 45.02 | β = 90 |
| c = 131.18 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 32 2 1 |
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 | MARMOSAIC 325 mm CCD | Flat collimating mirror, toroid focusing mirror | 2006-06-17 | M | SINGLE WAVELENGTH | |||||
| 2 | 2 | x-ray | 100 | CCD | MARMOSAIC 325 mm CCD | Flat collimating mirror, toroid focusing mirror | 2006-06-17 | M | MAD | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.97925 | SSRL | BL9-2 |
| 2 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.92522, 0.97934 | SSRL | BL9-2 |
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 | ||||||||
| 1,2 | 1.7 | 25.094 | 99.8 | 0.115 | 9.58 | 9.38 | 17704 | 37.034 | |||||||||||
| 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 | 1.7 | 1.76 | 99.8 | 0.97 | 1.99 | 7.01 | 1533 | ||||||||||||
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.7 | 25.094 | 17699 | 1361 | 99.86 | 0.185 | 0.18514 | 0.181 | 0.227 | RANDOM | 33.948 | ||||||
| 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] | |
| -0.63 | -0.32 | -0.63 | 0.95 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 28.465 |
| r_dihedral_angle_4_deg | 20.044 |
| r_dihedral_angle_3_deg | 14.219 |
| r_scangle_it | 7.64 |
| r_scbond_it | 5.706 |
| r_dihedral_angle_1_deg | 5.273 |
| r_mcangle_it | 3.507 |
| r_mcbond_it | 2.642 |
| r_angle_refined_deg | 1.451 |
| r_angle_other_deg | 1.025 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1197 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 65 |
| Heterogen Atoms | 4 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MolProbity | model building |
| REFMAC | refinement |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| SOLVE | phasing |
