3QXH
Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ADP and 8-aminocaprylic acid
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | 20% PEG3350; 150 MM NH4NO3; 100 MM BIS-TRIS; SOAKED WITH 10 MM ATP, 10 MM MGCL2, 10 MM 8-AMINOOCTANOIC ACID; IN SITU PROTEOLYSIS - CHYMOTRYPSIN, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.92 | 36.07 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 81.526 | α = 90 |
| b = 37.967 | β = 101.15 |
| c = 68.795 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 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 | SBC-3 | MIRROR | 2008-07-11 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.9793 | APS | 19-BM |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.36 | 50 | 97.7 | 0.026 | 0.026 | 47.3 | 4 | 43544 | 43544 | -3 | 11 | ||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 1.36 | 1.38 | 81.1 | 0.07 | 0.07 | 13.2 | 3.2 | 1735 | |||||||||||
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 | PDB entry 2QMO | 1.36 | 50 | 41354 | 41354 | 2190 | 97.59 | 0.11855 | 0.11855 | 0.11724 | 0.14245 | RANDOM | 8.869 | ||||
| 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] | |
| -0.04 | -0.15 | 0.14 | -0.16 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.27 |
| r_dihedral_angle_4_deg | 16.579 |
| r_dihedral_angle_3_deg | 11.717 |
| r_dihedral_angle_1_deg | 6.053 |
| r_scangle_it | 5.465 |
| r_scbond_it | 3.912 |
| r_mcangle_it | 2.584 |
| r_angle_other_deg | 2.307 |
| r_mcbond_other | 2.142 |
| r_rigid_bond_restr | 2.096 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1751 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 353 |
| Heterogen Atoms | 65 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-3000 | data collection |
| HKL-3000 | phasing |
| MOLREP | phasing |
| REFMAC | refinement |
| Coot | model building |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
