Crystal structure of dodecameric iron-containing heptosyltransferase TibC in complex with ADP-D-beta-D-heptose at 3.9 angstrom resolution
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4RAP | PDB ENTRY 4RAP |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 298 | 8% PEG 8000, 120mM magnesium acetate, 100mM MES buffer pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.02 | 69.38 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 88.292 | α = 90 |
| b = 313.196 | β = 101.26 |
| c = 164.695 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 200 | CCD | ADSC QUANTUM 315r | 2014-06-29 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRF BEAMLINE BL17U | 0.9791 | SSRF | BL17U |
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 | 3.88 | 20.04 | 98.7 | 76251 | 75852 | 2 | 2 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4RAP | 3.88 | 20.04 | 2 | 76851 | 75852 | 3995 | 98.7 | 0.2826 | 0.2826 | 0.28197 | 0.29 | 0.29457 | 0.3 | RANDOM | 148.073 | |
| 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] | |
| 10.59 | 3.42 | -8.69 | -2.39 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.314 |
| r_dihedral_angle_4_deg | 17.183 |
| r_dihedral_angle_3_deg | 16.192 |
| r_dihedral_angle_1_deg | 9.26 |
| r_chiral_restr | 0.422 |
| r_angle_other_deg | 0.397 |
| r_angle_refined_deg | 0.238 |
| r_bond_refined_d | 0.015 |
| r_gen_planes_refined | 0.012 |
| r_bond_other_d | 0.007 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 37107 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 504 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| Blu-Ice | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
