3DC4
Crystal structure of the Drosophila kinesin family member NOD in complex with ADP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 0.1 MES, 15% PEG 20000, Se-MET Derivative, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
2 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 0.1 MES, 15% PEG 20000, NATIVE PROTEIN, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.829 | α = 90 |
b = 75.715 | β = 90 |
c = 94.58 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | CCD | ADSC | TOROIDAL FOCUSING MIRROR | 2007-04-07 | M | MAD | ||||||
2 | 1 | x-ray | CCD | ADSC | TOROIDAL FOCUSING MIRROR | 2007-07-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X6A | 0.9790, 0.9796, 0.9184 | NSLS | X6A |
2 | SYNCHROTRON | NSLS BEAMLINE X6A | 0.9791 | NSLS | X6A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | |||||||
1,2 | 1.9 | 19 | 98.6 | 0.057 | 8.2 | 22.77 | 4.81 | 27088 | 1 | -3 | 30.315 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.9 | 2 | 98.8 | 0.342 | 35.4 | 4.9 | 4.88 | 18583 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MAD, MR | THROUGHOUT | 1.9 | 19 | 27088 | 1320 | 97.8 | 0.227 | 0.255 | RANDOM | 34.2 |
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] | |
2.81 | -7 | 4.18 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.8 |
c_improper_angle_d | 2.27 |
c_angle_deg | 1.6 |
c_bond_d | 0.006 |
c_mcbond_it | |
c_mcangle_it | |
c_scbond_it | |
c_scangle_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2247 |
Nucleic Acid Atoms | |
Solvent Atoms | 312 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
CNS | refinement |
SOLVE | phasing |
RESOLVE | phasing |
PDB_EXTRACT | data extraction |
CNS | phasing |