3MTC
Crystal Structure of INPP5B in complex with phosphatidylinositol 4-phosphate
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1I9Y | PDB ENTRY 1I9Y |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 22% polyacrylic acid, 0.02M magnesium chloride, 0.1M hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 5.51 | 77.67 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 133.761 | ¦Á = 90 |
| b = 133.761 | ¦Â = 90 |
| c = 133.761 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 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 315r | mirrors | 2009-12-17 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.97908 | ESRF | ID29 |
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 | 2.4 | 94.51 | 99.8 | 0.091 | 0.091 | 11.1 | 4.8 | 31433 | 31380 | 54 | |||||||||
| 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 | 2.4 | 2.53 | 99.9 | 0.698 | 0.698 | 2 | 4.5 | 4498 | |||||||||||
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 1I9Y | 2.4 | 47.29 | 29805 | 1580 | 99.88 | 0.17234 | 0.17062 | 0.20544 | RANDOM | 43.796 | ||||||
| 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 | 34.448 |
| r_dihedral_angle_4_deg | 17.662 |
| r_dihedral_angle_3_deg | 13.877 |
| r_dihedral_angle_1_deg | 6.384 |
| r_scangle_it | 2.881 |
| r_scbond_it | 1.736 |
| r_mcangle_it | 1.281 |
| r_angle_refined_deg | 1.278 |
| r_angle_other_deg | 0.806 |
| r_mcbond_it | 0.652 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2510 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 225 |
| Heterogen Atoms | 62 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| ADSC | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
