X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4E46 | PDB ENTRY 4E46 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 6.5 | PROTEIN WAS CRYSTALLIZED FROM 0.1 M MES/IMIDAZOLE PH 6.5, 10% (W/V) PEG 20000, 20% (V/V) PEG MME 500, 0.2 M DL-GLUTAMATIC ACID MONOHYDRATE, 0.02M DL-ALANINE, 0.02M GLYCINE, 0.02M DL-LYSINE MONOHYDROCHLORIDE AND 0.02M DL-SERINE | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.08 | 41 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 42.66 | α = 115.26 |
| b = 44.4 | β = 97.59 |
| c = 46.26 | γ = 109.52 |
| 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 | 100 | PIXEL | DECTRIS PILATUS 6M | 2015-02-01 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | Diamond | I04 | |
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 | 0.99 | 39.61 | 70.2 | 0.03 | 18.2 | 3.2 | 107099 | 2 | |||||||||||
| 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 | 0.99 | 1.02 | 6.5 | 0.33 | 2.1 | 1.3 | |||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4E46 | 0.99 | 39.61 | 101816 | 5283 | 70.18 | 0.11483 | 0.11405 | 0.12 | 0.12973 | 0.14 | RANDOM | 13.438 | ||||
| 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] | |
| 0.06 | 0.32 | 0.41 | -0.15 | 0.21 | -0.39 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.555 |
| r_sphericity_free | 28.241 |
| r_dihedral_angle_4_deg | 21.15 |
| r_dihedral_angle_3_deg | 13.011 |
| r_sphericity_bonded | 9.257 |
| r_dihedral_angle_1_deg | 6.003 |
| r_rigid_bond_restr | 3.756 |
| r_scangle_it | 2.348 |
| r_angle_refined_deg | 2.177 |
| r_scbond_it | 1.886 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2357 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 316 |
| Heterogen Atoms | 26 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| BALBES | phasing |
