5YJW
Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with the competitive inhibitor, stigmatellin.
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4G9K | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293 | 50mM Mes(pH 6.0), 34%(v/v) PEG 400, 100mM NaCl, 2% (v/v) ethylene glycol, 5%(v/v) glycerol |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3 | 59.05 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 116.67 | α = 90 |
| b = 128.456 | β = 90 |
| c = 86.711 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 2 2 21 |
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 | RAYONIX MX300HE | 2014-06-28 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.90000 | SPring-8 | BL44XU |
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 | 1.85 | 50 | 99.9 | 0.086 | 7.1 | 5.4 | 49022 | ||||||||||||
| 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 | 1.85 | 1.88 | 100 | 0.786 | 1.8 | 5 | |||||||||||||
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 | 4G9K | 1.85 | 29.48 | 49008 | 2632 | 92.52 | 0.18341 | 0.18227 | 0.2043 | RANDOM | 24.261 | ||||||
| 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] | |
| 0.01 | -0.04 | 0.03 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.089 |
| r_dihedral_angle_4_deg | 15.5 |
| r_dihedral_angle_3_deg | 13.426 |
| r_long_range_B_refined | 5.671 |
| r_dihedral_angle_1_deg | 5.626 |
| r_long_range_B_other | 5.389 |
| r_scangle_other | 1.789 |
| r_mcangle_it | 1.626 |
| r_mcangle_other | 1.626 |
| r_angle_refined_deg | 1.443 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3578 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 345 |
| Heterogen Atoms | 317 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
