X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3M4B | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 298 | Protein solution of: 2.2 mM protein with 1.65 mM Fe and 3 mM Zn premixed briefly prior to crystallisation. Drops were 1ul + 1 ul of protein solution and the following mother liquor: 30% PEG400, 0.1 M HEPES pH 7.5, 0.2 M (NH4)2SO4 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.74 | 55.17 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 126.7 | α = 90 |
| b = 126.7 | β = 90 |
| c = 167.8 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | H 3 2 |
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 PILATUS3 S 6M | Primary Mirror: flat internallyerror; Secondary Mirror: uncooled cyllindrical silicon bent into torroid | 2018-12-14 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.11583 | ALS | 8.3.1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.85 | 91.83 | 100 | 0.096 | 0.101 | 0.031 | 0.999 | 13.7 | 10.32 | 85783 | 35.57 | ||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 1.85 | 1.9 | 100 | 2.377 | 2.498 | 0.468 | 1.04 | 10.553 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FREE R-VALUE | 3M4B | 1.85 | 91.83 | 1.34 | 85755 | 2946 | 99.96 | 0.1836 | 0.1826 | 0.18 | 0.2106 | 0.21 | Random selection | 41.52 | |||
| 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 |
| f_dihedral_angle_d | 16.8505 |
| f_angle_d | 0.8666 |
| f_chiral_restr | 0.0463 |
| f_bond_d | 0.0078 |
| f_plane_restr | 0.0053 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3296 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 342 |
| Heterogen Atoms | 239 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XDS | data reduction |
| XSCALE | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| PHASER | phasing |
