X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2EVA | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.7 | 294 | 1.7M sodium potassium phosphate, 20%(v/v) Glycerol as cryoprotectant |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.99 | 69.18 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 58.03 | α = 90 |
| b = 133.22 | β = 90 |
| c = 146.75 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 2 2 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 | CCD | ADSC QUANTUM 315r | 2009-10-19 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1.0000 | Photon Factory | BL-5A |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.61 | 41.93 | 99.2 | 0.094 | 0.101 | 0.038 | 18.7 | 7.2 | 17613 | 17613 | |||||||||
| 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 | 2.61 | 2.68 | 96.3 | 0.873 | 0.9 | 7.1 | |||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2EVA | 2.61 | 41.93 | 16721 | 892 | 99.21 | 0.1826 | 0.1806 | 0.19 | 0.221 | 0.23 | RANDOM | 59.236 | ||||
| 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] | |
| -6.06 | -1.34 | 7.4 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 40.581 |
| r_dihedral_angle_4_deg | 16.837 |
| r_dihedral_angle_3_deg | 15.652 |
| r_mcangle_it | 8.368 |
| r_dihedral_angle_1_deg | 8.286 |
| r_mcbond_other | 5.424 |
| r_mcbond_it | 5.419 |
| r_angle_refined_deg | 1.95 |
| r_angle_other_deg | 1.087 |
| r_chiral_restr | 0.108 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2224 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 36 |
| Heterogen Atoms | 42 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XDS | data processing |
| SCALA | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
