5I5Q
Re refinement of 4mwn.
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4MWN | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | BATCH MODE | 4.7 | 294 | CRYSTALLIZATION CONDITIONS: 40MG HEWL CO-CRYSTALLISED WITH 2.6MG CISPLATIN, WITH THE PLATINUM COMPOUNDS BEING IN A 3-FOLD MOLAR EXCESS TO THE PROTEIN, 462.5 UL OF A 0.02M NAAC SOLUTION ALONG WITH 462.5 UL OF A 0.5M NANO3 SOLUTION WAS USED WITH 75 UL DMSO ADDED, BATCH, PH 4.7, EVAPORATION, TEMPERATURE 294K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.84 | 33.2 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 27.346 | α = 88.04 |
| b = 32.134 | β = 71.17 |
| c = 34.296 | γ = 68.35 |
| 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 | 294 | CCD | APEX II CCD | 2012-12-15 | 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 | 1.42 | 32.31 | 94.8 | 0.145 | 6.8 | 5.7 | 18176 | ||||||||||||
| 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 | 1.42 | 1.51 | 98.5 | 0.554 | 1.1 | 2 | |||||||||||||
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 | 4mwn | 1.42 | 32.31 | 18176 | 984 | 99.21 | 0.18734 | 0.18462 | 0.23687 | RANDOM | 15.451 | ||||||
| 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] | |
| 0.1 | 0.28 | -0.13 | -0.26 | -0.02 | 0.24 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.054 |
| r_sphericity_free | 22.052 |
| r_dihedral_angle_4_deg | 18.644 |
| r_dihedral_angle_3_deg | 12.905 |
| r_sphericity_bonded | 7.435 |
| r_dihedral_angle_1_deg | 6.482 |
| r_rigid_bond_restr | 5.369 |
| r_scangle_other | 3.545 |
| r_scbond_it | 3.466 |
| r_scbond_other | 3.383 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 992 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 37 |
| Heterogen Atoms | 19 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| SAINT | data reduction |
| APEX | data scaling |
| PHASER | phasing |
