3EKS
Crystal Structure of Monomeric Actin bound to Cytochalasin D
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP, MICROSEEDING, MACROSEEDING | 5.2 | 277 | 15.5% MPD, 0.1M sodium acetate, 0.1M NaCl, 0.02M CaCl2, pH 5.2, VAPOR DIFFUSION, SITTING DROP, MICROSEEDING, MACROSEEDING, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.46 | 49.97 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 195.207 | α = 90 |
| b = 54.634 | β = 90.65 |
| c = 38.569 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 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 | IMAGE PLATE | MAR scanner 345 mm plate | 2008-01-28 | M | SINGLE WAVELENGTH | ||||||
| 2 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | 2008-03-28 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RUH3R | 1.5418 | ||
| 2 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1.03320 | APS | 23-ID-B |
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 | 1.8 | 50 | 81.3 | 0.125 | 12.6 | 3.1 | 38182 | 31036 | |||||||||||
| 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) | |||||||||||
| 1.8 | 1.85 | 54.8 | 0.363 | 1.89 | 2.2 | 3193 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | THROUGHOUT | 1.8 | 50 | 28761 | 28761 | 2500 | 75.3 | 0.25 | 0.25 | 0.237 | 0.284 | random | 36.535 | ||||||
| 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] | |
| 6.809 | 11.065 | 7.169 | -13.978 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_scangle_it | 2.937 |
| c_mcangle_it | 2.312 |
| c_scbond_it | 2.088 |
| c_mcbond_it | 1.485 |
| c_angle_deg | 1.27 |
| c_bond_d | 0.0073 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2900 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 271 |
| Heterogen Atoms | 70 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| CNS | refinement |
| PDB_EXTRACT | data extraction |
| Blu-Ice | data collection |
| EPMR | phasing |
