X-ray structure of Fe(III)-bicarbonates-ttfbpa, a ferric ion-binding protein from thermus thermophilus HB8
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 5.5 | 0.1M BIS-TRIS (PH 5.5), 0.2M SODIUM CHLORIDE, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.89 | 34.8 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 40.17 | α = 90 |
| b = 101.02 | β = 90 |
| c = 134.61 | 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 225 mm CCD | 2011-07-08 | M | SINGLE WAVELENGTH | ||||||
| 2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 270 | 2011-11-04 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL32XU | 1.0000 | SPring-8 | BL32XU |
| 2 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NE3A | 1.7209 | Photon Factory | AR-NE3A |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 45 | 99.4 | 62381 | 1 | ||||||||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.7 | 19.98 | 58159 | 3103 | 99.91 | 0.20342 | 0.20133 | 0.2 | 0.24258 | 0.24 | RANDOM | 16.618 | |||||
| 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] | |
| 0.08 | -0.03 | -0.06 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.495 |
| r_dihedral_angle_4_deg | 14.83 |
| r_dihedral_angle_3_deg | 14.344 |
| r_dihedral_angle_1_deg | 5.28 |
| r_angle_refined_deg | 1.292 |
| r_chiral_restr | 0.079 |
| r_bond_refined_d | 0.009 |
| r_gen_planes_refined | 0.006 |
| r_bond_other_d | |
| r_angle_other_deg | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4785 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 513 |
| Heterogen Atoms | 18 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| ADSC | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| XDSME | data reduction |
| XDSME | data scaling |
