7OOW
Crystal structure of PIM1 in complex with ARC-1415
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2J2I | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 277.15 | 15%(w/v) PEG 10000, 0.2M magnesium chloride, 0.1M tris pH 7.9 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.18 | 61.37 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 98.614 | α = 90 |
| b = 98.614 | β = 90 |
| c = 80.729 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 65 |
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 PILATUS3 6M | 2013-07-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97625 | Diamond | I03 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.95 | 42.7 | 99.9 | 0.099 | 0.12 | 0.052 | 0.995 | 11 | 5.1 | 32555 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.95 | 2.02 | 99.9 | 0.948 | 1.121 | 0.494 | 0.734 | 3.1 | 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 | 2j2i | 1.95 | 42.7 | 30996 | 1547 | 99.87 | 0.1614 | 0.1602 | 0.1838 | RANDOM | 33.68 | ||||||
| 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] | |
| 0.47 | 0.24 | 0.47 | -1.53 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 28.809 |
| r_dihedral_angle_4_deg | 15.576 |
| r_dihedral_angle_3_deg | 13.567 |
| r_dihedral_angle_1_deg | 6.735 |
| r_angle_refined_deg | 1.412 |
| r_angle_other_deg | 1.312 |
| r_chiral_restr | 0.075 |
| r_bond_refined_d | 0.013 |
| r_gen_planes_refined | 0.01 |
| r_bond_other_d | 0.001 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2217 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 214 |
| Heterogen Atoms | 110 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| Aimless | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| PHASER | phasing |
