4LPB
Crystal structure of a topoisomerase ATPase inhibitor
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 18-25% Peg4000, 0.2M Ammonium Acetate, 0.1M MIB pH 7, hanging drop, inhibitor soak, temperature 293K, VAPOR DIFFUSION, HANGING DROP |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.16 | 43.09 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 73.411 | α = 90 |
| b = 94.706 | β = 90 |
| c = 61.18 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 2 2 21 |
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 | RAYONIX MX-225 | monochromator | 2007-10-12 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 31-ID | 1.000 | APS | 31-ID |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.608 | 22.092 | 99.9 | 0.093 | 0.093 | 14.7 | 7.1 | 21859 | 21859 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 1.75 | 1.84 | 100 | 0.577 | 0.577 | 1.2 | 7.2 | 3152 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.75 | 22.08 | 21842 | 1117 | 99.9 | 0.1951 | 0.1936 | 0.2236 | RANDOM | 22.675 | |||||||
| 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] | |
| 0.08 | -0.56 | 0.49 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 29.434 |
| r_dihedral_angle_4_deg | 12.423 |
| r_dihedral_angle_3_deg | 11.327 |
| r_dihedral_angle_1_deg | 4.656 |
| r_scangle_it | 1.7 |
| r_scbond_it | 1.113 |
| r_angle_refined_deg | 1.079 |
| r_angle_other_deg | 0.771 |
| r_mcangle_it | 0.684 |
| r_mcbond_it | 0.446 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1485 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 120 |
| Heterogen Atoms | 33 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SCALA | data scaling |
| AMoRE | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
