Crystal structure of Ser/Thr kinase Pim1 in complex with 10-DEBC derivatives
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1YWV | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, HANGING DROP | 8 | 291 | 0.4M potassium sodium tartrate tetrahydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 3.6 | 65.87 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 98.425 | α = 90 |
| b = 98.425 | β = 90 |
| c = 80.99 | γ = 120 |
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 291 | IMAGE PLATE | RIGAKU RAXIS IV++ | | 2018-02-20 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 0.97918 | | |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | injection |
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 | 1.95 | 85.24 | 99.8 | 0.058 | 1 | 44.72 | 11.2 | | 32642 | | | |
| 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 | 1.95 | 1.998 | | | 1.038 | 0.787 | | | |
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 | 1YWV | 1.95 | 85.24 | 31072 | 1540 | 99.68 | 0.1933 | 0.1925 | 0.2 | 0.2094 | 0.21 | RANDOM | 42.887 |
| 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 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_2_deg | 37.248 |
| r_dihedral_angle_4_deg | 19.03 |
| r_dihedral_angle_3_deg | 13.337 |
| r_dihedral_angle_1_deg | 5.626 |
| r_angle_other_deg | 3.603 |
| r_angle_refined_deg | 1.345 |
| r_chiral_restr | 0.086 |
| r_bond_refined_d | 0.01 |
| r_gen_planes_other | 0.007 |
| r_gen_planes_refined | 0.006 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_2_deg | 37.248 |
| r_dihedral_angle_4_deg | 19.03 |
| r_dihedral_angle_3_deg | 13.337 |
| r_dihedral_angle_1_deg | 5.626 |
| r_angle_other_deg | 3.603 |
| r_angle_refined_deg | 1.345 |
| r_chiral_restr | 0.086 |
| r_bond_refined_d | 0.01 |
| r_gen_planes_other | 0.007 |
| r_gen_planes_refined | 0.006 |
| r_bond_other_d | |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2209 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 59 |
| Heterogen Atoms | 24 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| PHASES | phasing |
