Structural Genomics, the crystal structure of a putative transcriptional regulator GntR from Rhodococcus sp. RHA1
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 298 | 35% Tacsimate, 0.1M Sodium Acetate, 2% PEG5000 MME, 2mM Cysteine, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.97 | 58.54 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 108.052 | α = 90 |
| b = 108.052 | β = 90 |
| c = 107.26 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 4 2 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 | CCD | ADSC QUANTUM 315 | mirror | 2006-04-19 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97932 | APS | 19-ID |
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 | 38.21 | 97.9 | 0.076 | 31.84 | 7.4 | 16123 | 16123 | |||||||||||
| 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 | 2.25 | 81.1 | 0.54 | 2.44 | 4.9 | 869 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | 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 | SAD | THROUGHOUT | 2.2 | 38.21 | 15289 | 15289 | 815 | 97.86 | 0.19673 | 0.19673 | 0.1941 | 0.1952 | 0.24851 | 0.2426 | RANDOM | 43.5 | |||
| 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] | |
| -0.01 | -0.01 | 0.01 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.303 |
| r_dihedral_angle_4_deg | 22.403 |
| r_dihedral_angle_3_deg | 19.604 |
| r_scangle_it | 7.243 |
| r_dihedral_angle_1_deg | 6.737 |
| r_scbond_it | 4.701 |
| r_mcangle_it | 2.965 |
| r_angle_refined_deg | 2.599 |
| r_mcbond_it | 2.148 |
| r_nbtor_refined | 0.312 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1618 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 88 |
| Heterogen Atoms | 4 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| HKL-3000 | phasing |
| SHELXE | model building |
| SOLVE | phasing |
| RESOLVE | phasing |
| ARP/wARP | model building |
