3F2W
Crystal structure of the FMn riboswitch bound to FMN, Ba2+ soak.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 0.1 M MES-Na pH 6.5 10% PEG 4000 0.1 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.79 | 55.91 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 71.003 | α = 90 |
| b = 71.003 | β = 90 |
| c = 139.745 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 31 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 | ADSC QUANTUM 315 | 2007-11-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.6 | NSLS | X29A |
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 | 3.45 | 20 | 98.9 | 0.105 | 22.1 | 9.2 | 5754 | 5691 | |||||||||||
| 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 | 3.45 | 3.57 | 92.8 | 0.578 | 3.2 | 4.6 | 556 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3F2Q | 3.45 | 20 | 5449 | 5385 | 258 | 98.83 | 0.18249 | 0.18249 | 0.18089 | 0.21738 | RANDOM | 110.093 | ||||
| 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] | |
| -2.61 | -1.31 | -2.61 | 3.92 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_angle_refined_deg | 1.043 |
| r_scangle_it | 0.654 |
| r_scbond_it | 0.387 |
| r_nbtor_refined | 0.277 |
| r_metal_ion_refined | 0.206 |
| r_nbd_refined | 0.16 |
| r_xyhbond_nbd_refined | 0.137 |
| r_symmetry_vdw_refined | 0.092 |
| r_chiral_restr | 0.047 |
| r_bond_refined_d | 0.004 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | |
| Nucleic Acid Atoms | 2353 |
| Solvent Atoms | 1 |
| Heterogen Atoms | 54 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CBASS | data collection |
| MOLREP | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
