1Z2B
Tubulin-colchicine-vinblastine: stathmin-like domain complex
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1SA0 | pdb entry 1SA0 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7 | 291 | PEG, PIPES BUFFER, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K. THE CRYSTAL OF TUBULIN-COLCHICINE:RB3-SLD COMPLEX WAS SOAKED WITH A 2 MILLI-MOLAR VINBLASTINE SOLUTION FOR 24 HOURS., pH 7.00 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.81 | 68 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 324.852 | α = 90 |
| b = 324.852 | β = 90 |
| c = 54.208 | 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 | CCD | ADSC | 2002-06-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 | |
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 | 4.1 | 40 | 94.8 | 0.04 | 25 | 3.26 | 25286 | ||||||||||||
| 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 | 4.1 | 4.2 | 76.6 | 0.33 | 2.5 | 2.25 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 1SA0 | 4.1 | 20 | 25034 | 23765 | 1269 | 95.39 | 0.21243 | 0.20943 | 0.26886 | RANDOM | 117.488 | |||||
| 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] | |
| -0.77 | -0.38 | -0.77 | 1.15 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_1_deg | 8.541 |
| r_angle_refined_deg | 1.906 |
| r_symmetry_vdw_refined | 0.344 |
| r_nbd_refined | 0.3 |
| r_metal_ion_refined | 0.279 |
| r_xyhbond_nbd_refined | 0.213 |
| r_symmetry_hbond_refined | 0.131 |
| r_chiral_restr | 0.12 |
| r_bond_refined_d | 0.017 |
| r_gen_planes_refined | 0.005 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 13932 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 241 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| AMoRE | phasing |
| REFMAC | refinement |
