3D7V
Crystal structure of Mcl-1 in complex with an Mcl-1 selective BH3 ligand
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5.75 | 298 | 0.2M Zinc Acetate, 0.2M Imidazole, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.51 | 51.06 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 51.171 | α = 90 |
| b = 69.635 | β = 90 |
| c = 120.654 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 2 2 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IV++ | Capillary optics (AXCO) | 2006-03-24 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.5418 | ||
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 | 2.03 | 60.3 | 98.71 | 0.044 | 3.2 | 13365 | 5.6 | ||||||||||||
| 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) | |||||||||||
| 2.03 | 2.1 | 96.1 | 0.204 | 3.1 | 3.1 | 1357 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 | 2NL9 | 2.03 | 50 | 2 | 13365 | 710 | 98.71 | 0.19441 | 0.19201 | 0.24108 | RANDOM | 27.253 | |||||
| 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 | -0.51 | 0.99 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.358 |
| r_dihedral_angle_4_deg | 18.131 |
| r_dihedral_angle_3_deg | 15.074 |
| r_dihedral_angle_1_deg | 4.209 |
| r_scangle_it | 3.658 |
| r_scbond_it | 2.363 |
| r_mcangle_it | 1.624 |
| r_angle_refined_deg | 1.194 |
| r_mcbond_it | 0.967 |
| r_symmetry_hbond_refined | 0.362 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1357 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 120 |
| Heterogen Atoms | 4 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| CrystalClear | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
