X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4D06 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 6.8 mg/ml CHI 50 mM Na phosphate, pH 6.8. Precipitant 1.5 M (NH4)2SO4, 0.2 M NaCl, 0.1 M HEPES pH 7.5. Soaking for 10 min in 2.5 mM taxifolin (2.5% ethanol) |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.88 | 75 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 186.359 | α = 90 |
| b = 204.683 | β = 90 |
| c = 561.904 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 21 21 21 |
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 | RIGAKU SATURN 92 | 2016-05-27 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.5418 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim 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 | 2.95 | 33.96 | 98.8 | 0.289 | 3.92 | 3.92 | 222025 | 47.3 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.95 | 3.05 | 95.1 | 0.76 | 3.06 | ||||||||||||||
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 (All) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4D06 | 3 | 33.955 | 211050 | 4272 | 98.833 | 0.249 | 0.2489 | 0.25 | 0.2681 | 0.27 | 58.08 | |||||
| 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] | |
| 0.868 | -0.211 | -0.657 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_6_deg | 16.371 |
| r_dihedral_angle_3_deg | 14.895 |
| r_dihedral_angle_2_deg | 10.163 |
| r_dihedral_angle_1_deg | 7.771 |
| r_lrange_it | 6.62 |
| r_lrange_other | 6.62 |
| r_scangle_it | 3.738 |
| r_scangle_other | 3.649 |
| r_mcangle_it | 3.34 |
| r_mcangle_other | 3.34 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 38166 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 4 |
| Heterogen Atoms | 1083 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| CrystalClear | data reduction |
| d*TREK | data scaling |
| PHASER | phasing |
