3IVG
Crystal structure of pantothenate synthetase in complex with 2-(2-((benzofuran-2-sulfonamido)methyl)-5-methoxy-1H-indol-1-yl)acetic acid
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 12% PEG3000, 150 mM Li2SO4, 0.1 M imidazole, 2% ethanol, 10% glycerol, 20 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.18 | 43.68 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 48.33 | ¦Á = 90 |
| b = 70.71 | ¦Â = 99.6 |
| c = 81.85 | ¦Ã = 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 | 100 | CCD | ADSC QUANTUM 315r | 2009-04-18 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.93 | ESRF | ID14-4 |
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 | 1.95 | 80 | 99.4 | 0.09 | 11.4 | 3.6 | 39770 | 22.9 | |||||||||||
| 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 | 1.95 | 2.01 | 99.9 | 0.529 | 11.4 | ||||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.95 | 44.4 | 37529 | 1982 | 99.39 | 0.17474 | 0.17221 | 0.22133 | RANDOM | 27.723 | |||||||
| 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] | |
| 1.17 | -0.33 | 0.48 | -1.76 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 38.632 |
| r_dihedral_angle_4_deg | 15.504 |
| r_dihedral_angle_3_deg | 14.496 |
| r_dihedral_angle_1_deg | 5.945 |
| r_scangle_it | 3.96 |
| r_scbond_it | 2.575 |
| r_mcangle_it | 1.742 |
| r_angle_refined_deg | 1.56 |
| r_mcbond_it | 1.049 |
| r_nbtor_refined | 0.307 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4129 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 432 |
| Heterogen Atoms | 85 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| ADSC | data collection |
| PHASES | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
