8BQF
Adenylate Kinase L107I MUTANT
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 292 | 7.5% PEG 3,350, 7.5% PEG 4,000, 7.5% PEG 2,000, 7.5% PEG 5,000 monomethyl ether, 0.07M ammonium nitrate, 2.5% ethylene glycol and 0.05M MES pH=7. |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.33 | 47.11 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 77.975 | α = 90 |
| b = 84.49 | β = 90 |
| c = 218.493 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 2 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 | PIXEL | RIGAKU HyPix-3000 | 2022-03-20 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU | 1.3405 | ||
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 | 2.05 | 21.04 | 99.69 | 0.1043 | 0.1117 | 0.03909 | 0.995 | 20.47 | 8.1 | 93318 | |||||||||
| 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 | 2.05 | 2.123 | 100 | 0.4044 | 0.435 | 0.1585 | 0.931 | 4.39 | 7.4 | ||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 7F7U | 2.05 | 21.04 | 93318 | 4792 | 99.8 | 0.22073 | 0.21882 | 0.25789 | RANDOM | 27.461 | ||||||
| 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] | |
| 0.1 | 1.35 | -1.45 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 27.006 |
| r_dihedral_angle_3_deg | 16.319 |
| r_dihedral_angle_4_deg | 14.31 |
| r_dihedral_angle_1_deg | 7.044 |
| r_long_range_B_other | 5.588 |
| r_long_range_B_refined | 5.586 |
| r_scangle_other | 4.147 |
| r_mcangle_it | 3.511 |
| r_mcangle_other | 3.51 |
| r_scbond_it | 2.688 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 9486 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 223 |
| Heterogen Atoms | 338 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| CrysalisPro | data reduction |
| CrysalisPro | data scaling |
| PHASER | phasing |
