Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5ADZ | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 7.5 | 293 | PEG 1500 20%, HEPES, PH 7.5, 100 MM |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.26 | 45.49 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 147.958 | α = 90 |
| b = 120.644 | β = 95.27 |
| c = 148.16 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 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 | PIXEL | DECTRIS PILATUS 300K | 2015-06-09 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SLS BEAMLINE X06DA | 0.8729 | SLS | X06DA |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 2.9 | 48 | 100 | 0.181 | 0.994 | 11.2 | 7.8 | 57552 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 2.9 | 2.98 | 100 | 0.8 | 0.826 | 2.9 | 8.1 | ||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 5ADZ | 2.9 | 48 | 54617 | 2934 | 99.97 | 0.22057 | 0.21858 | 0.22 | 0.25817 | 0.26 | RANDOM | 48.02 | ||||
| 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] | |
| -0.89 | -1.93 | 2.42 | -1.15 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.683 |
| r_dihedral_angle_3_deg | 16.939 |
| r_dihedral_angle_4_deg | 16.315 |
| r_long_range_B_refined | 8.22 |
| r_long_range_B_other | 8.22 |
| r_dihedral_angle_1_deg | 6.363 |
| r_scangle_other | 5.474 |
| r_mcangle_it | 5.427 |
| r_mcangle_other | 5.427 |
| r_mcbond_it | 3.367 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 17058 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 287 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| Aimless | data scaling |
| REFMAC | phasing |
