Crystal structure of Putative transcriptional regulator (JANN_22DEC04_CONTIG27_REVISED_GENE3569) from Jannaschia sp. CCS1 at 2.81 A resolution
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | 20.0000% polyethylene glycol 3350, 0.2500M lithium sulfate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.47 | 50.28 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 69.953 | α = 90 |
| b = 81.722 | β = 90 |
| c = 199.921 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 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 | MARMOSAIC 325 mm CCD | Flat collimating mirror, toroid focusing mirror | 2007-03-16 | M | MAD | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.97939,0.91162,0.97925 | 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 | 2.81 | 46.932 | 98.5 | 0.124 | 8.29 | 28370 | -3 | 63.565 | |||||||||||
| 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 | 2.81 | 2.91 | 91 | 0.757 | 2.3 | ||||||||||||||
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 | MAD | THROUGHOUT | 2.81 | 46.932 | 28332 | 1430 | 0.202 | 0.199 | 0.21 | 0.245 | 0.26 | RANDOM | 68.579 | ||||||
| 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] | |
| 3.065 | 12.437 | -15.502 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| o_improper_angle_d | 17.89 |
| o_dihedral_angle_d | 2.43 |
| o_angle_deg | 1.12 |
| o_bond_d | 0.01 |
| o_bond_d_na | |
| o_bond_d_prot | |
| o_angle_d | |
| o_angle_d_na | |
| o_angle_d_prot | |
| o_angle_deg_na | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 7625 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 34 |
| Heterogen Atoms | 50 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| BUSTER | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
| MolProbity | model building |
