5IDD
Comment on S. W. M. Tanley and J. R. Helliwell Structural dynamics of cisplatin binding to histidine in a protein Struct. Dyn. 1, 034701 (2014) regarding the refinement of 4mwk, 4mwm, 4mwn and 4oxe and the method we have adopted.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | BATCH MODE | 4.7 | 293 | CRYSTALLIZATION CONDITIONS: 40MG HEWL (2.7MM) CO-CRYSTALLISED WITH 3MG CARBOPLATIN (8.1MM). 462.5 microL OF A 0.02M NAAC SOLUTION ALONG REMARK 280 WITH 462.5 microL OF A 0.5M NANO3 SOLUTION WAS USED WITH 75 microL DMSO. |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.79 | 31.29 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 26.957 | α = 88.76 |
| b = 31.794 | β = 71.99 |
| c = 34.055 | γ = 68.33 |
| Symmetry | |
|---|---|
| Space Group | P 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 200 | CCD | APEX II CCD | CONFOCAL MIRROR OPTICS | 2012-11-18 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | BRUKER AXS MICROSTAR-H | 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 | 1.13 | 32.21 | 94.1 | 0.086 | 7.2 | 2.9 | 35817 | ||||||||||||
| 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 | 1.13 | 1.16 | 77 | 0.31 | 2 | 1.1 | |||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4oxe | 1.13 | 32.21 | 33282 | 1762 | 94.09 | 0.17964 | 0.1775 | 0.21982 | RANDOM | 12.268 | ||||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.443 |
| r_sphericity_free | 27.301 |
| r_dihedral_angle_4_deg | 19.942 |
| r_sphericity_bonded | 11.116 |
| r_dihedral_angle_3_deg | 10.158 |
| r_rigid_bond_restr | 8.793 |
| r_dihedral_angle_1_deg | 6.948 |
| r_scangle_other | 4.131 |
| r_long_range_B_refined | 3.87 |
| r_long_range_B_other | 3.869 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 986 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 79 |
| Heterogen Atoms | 41 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| SAINT | data reduction |
| APEX 2 | data scaling |
| PHASER | phasing |
