X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5KBN | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.2 | 295 | 50 mM ADA-NaOH, 50 mM LiNO3, 34% PEG 400 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 5.33 | 76.91 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 105.441 | α = 90 |
| b = 105.441 | β = 90 |
| c = 183.015 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 77 | CCD | ADSC QUANTUM 315r | 2015-06-23 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | 0.999 | ALS | 8.2.2 |
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 | 3 | 91.53 | 100 | 0.162 | 0.165 | 0.031 | 1 | 21.1 | 28.1 | 21435 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 3 | 3.18 | 100 | 1.983 | 2.018 | 0.372 | 0.842 | 29.1 | |||||||||||
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 | 5kbn | 3 | 91.53 | 20295 | 1077 | 99.91 | 0.2247 | 0.2233 | 0.23 | 0.2494 | 0.26 | RANDOM | 85.372 | ||||
| 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] | |
| 1.96 | 1.96 | -3.91 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.377 |
| r_dihedral_angle_4_deg | 24.306 |
| r_dihedral_angle_3_deg | 16.799 |
| r_dihedral_angle_1_deg | 6.659 |
| r_angle_refined_deg | 2.069 |
| r_angle_other_deg | 1.116 |
| r_chiral_restr | 0.121 |
| r_bond_refined_d | 0.019 |
| r_gen_planes_refined | 0.01 |
| r_bond_other_d | 0.002 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3361 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 20 |
| Heterogen Atoms | 5 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
