5XJB
The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with ADP-Mg-BeFx
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 297 | potassium sodium tartrate tetrahydrate, MES, pH 6.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.9 | 57.62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.452 | α = 90 |
b = 166.593 | β = 90 |
c = 75.5 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | 98 | PIXEL | DECTRIS PILATUS3 S 6M | 2017-02-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 0.98 | Photon Factory | BL-17A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim 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 | 3.1 | 30 | 99.9 | 0.07 | 0.029 | 23.2 | 6.5 | 21151 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.1 | 3.18 | 100 | 0.639 | 0.23 | 2.5 | 6.5 |
Refinement
Statistics | |||||||||||||||||||
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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 | 1V8K | 3.1 | 30 | 20045 | 1061 | 99.78 | 0.2042 | 0.2012 | 0.2614 | RANDOM | 79.629 |
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] | |
10.25 | -6.08 | -4.17 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.541 |
r_dihedral_angle_4_deg | 18.764 |
r_dihedral_angle_3_deg | 16.921 |
r_dihedral_angle_1_deg | 9.931 |
r_angle_refined_deg | 1.694 |
r_angle_other_deg | 1.27 |
r_chiral_restr | 0.087 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5275 |
Nucleic Acid Atoms | |
Solvent Atoms | 5 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |