2Y77
Structure of Mycobacterium tuberculosis type II dehydroquinase complexed with (1R,4S,5R)-3-(benzo(b)thiophen-2-ylmethoxy)-1,4,5- trihydroxy-2-(thiophen-2-ylmethyl)cyclohex-2-enecarboxylate
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7.5 | 33% (V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.3 M AMMONIUM SULPHATE, 0.1 M HEPES-NAOH PH 7.5 50 MM TRIS-HCL PH 7.5, 1 MM 2-MERCAPTOETHANOL, 1 MM EDTA, 200 MM SODIUM CHLORIDE, 12.5 MM SODIUM (1R,4S,5R)- 3-(1-BENZOTHIOPHEN-2-YLMETHOXY)-1,4,5-TRIHYDROXY-2-(THIOPHEN- 2-YLMETHYL) CYCLOHEX-2-ENE-1-CARBOXYLATE. | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.7 | 54 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 125.8 | α = 90 |
| b = 125.8 | β = 90 |
| c = 125.8 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | F 2 3 |
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 210r | 1 - A RD COATED FLAT MIRROR - 2 - A RD COATED TOROIDAL MIRROR | 2009-11-20 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE BM16 | ESRF | BM16 | |
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 | 1.4 | 31.5 | 94.3 | 0.06 | 7.5 | 7.5 | 30571 | 16.8 | |||||||||||
| 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 | 1.4 | 1.48 | 64.9 | 0.4 | 2 | 1.6 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1H0S | 1.5 | 20 | 24982 | 1330 | 99.92 | 0.16244 | 0.16133 | 0.18388 | RANDOM | 11.457 | ||||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.486 |
| r_dihedral_angle_4_deg | 13.597 |
| r_dihedral_angle_3_deg | 12.577 |
| r_dihedral_angle_1_deg | 5.538 |
| r_scangle_it | 3.451 |
| r_scbond_it | 2.327 |
| r_mcangle_it | 1.544 |
| r_angle_refined_deg | 1.539 |
| r_mcbond_it | 0.995 |
| r_rigid_bond_restr | 0.923 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1016 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 107 |
| Heterogen Atoms | 49 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
