3O8M
Crystal structure of monomeric KlHxk1 in crystal form XI with glucose bound (closed state)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 292 | 0.2microL reservoir + 0.2microL protein, reservoir: 20% PEG6000, 1M LiCl, 0.1M Hepes pH 7.0, protein: 6.6mg/ml KlHxk1, 10mM Tris pH 7.4, 1mM EDTA, 1mM DTT, 0.5mM PMSF, 10mM AMPPNP, 10mM Glucose, 10mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.36 | 47.92 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 64.575 | α = 90 |
| b = 75.599 | β = 90 |
| c = 103.857 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 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 | MARMOSAIC 225 mm CCD | 1st mirror: Silicon, active surface 50 nm Rh-coated, 2nd mirror: Glas, active surface 50 nm Rh-coated | 2008-07-15 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.91841 | BESSY | 14.2 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | 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 | 1.42 | 30 | 96.2 | 0.05 | 22.6 | 7.1 | 96547 | 92838 | -3 | 23.1 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1.42 | 1.46 | 72.7 | 0.491 | 2.9 | 4.1 | 5134 | |||||||||||||
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 | PDB entry 3O08 | 1.42 | 29.7 | 91406 | 1367 | 96.19 | 0.18694 | 0.18651 | 0.21578 | RANDOM | 18.898 | ||||||
| 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] | |
| -0.35 | -0.99 | 1.34 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.218 |
| r_dihedral_angle_4_deg | 16.89 |
| r_dihedral_angle_3_deg | 12.534 |
| r_dihedral_angle_1_deg | 6.565 |
| r_scangle_it | 4.365 |
| r_scbond_it | 3.257 |
| r_angle_refined_deg | 2.313 |
| r_mcangle_it | 2.224 |
| r_mcbond_it | 1.679 |
| r_chiral_restr | 0.163 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3669 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 611 |
| Heterogen Atoms | 28 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MAR345 | data collection |
| AMoRE | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
