2X7G
Structure of human serine-arginine-rich protein-specific kinase 2 (SRPK2) bound to purvalanol B
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1WBP | PDB ENTRY 1WBP |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 4.75 | 0.5M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE PH4.75 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.6 | 65.82 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 110.31 | α = 90 |
| b = 110.31 | β = 90 |
| c = 90.59 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 31 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 | CCD | RAYONIX | 2009-09-28 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | Diamond | I24 | |
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 | 2.5 | 45.21 | 99.7 | 0.13 | 6.5 | 3.2 | 22306 | 43.1 | |||||||||||
| 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 | 2.5 | 2.64 | 99.6 | 0.59 | 2 | 3.2 | |||||||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1WBP | 2.5 | 45 | 21171 | 1135 | 99.46 | 0.18615 | 0.18292 | 0.18 | 0.24868 | 0.24 | RANDOM | 16.352 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| 0.08 | 0.04 | 0.08 | -0.12 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.143 |
| r_dihedral_angle_4_deg | 16.742 |
| r_dihedral_angle_3_deg | 14.205 |
| r_scangle_it | 9.999 |
| r_scbond_it | 7.692 |
| r_dihedral_angle_1_deg | 5.792 |
| r_mcangle_it | 4.091 |
| r_mcbond_it | 2.452 |
| r_angle_refined_deg | 1.368 |
| r_angle_other_deg | 0.865 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2765 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 111 |
| Heterogen Atoms | 93 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
