7UR2
Crystal structure of the Sec14 domain of the RhoGEF Kalirin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 100 mM sodium cacodylate, pH 6.5, 0.2 M ammonium sulfate, 20-25% PEG3350, 0.2 M sodium chloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.65 | 53.54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 72.16 | α = 81.09 |
b = 82.42 | β = 71.79 |
c = 83.27 | γ = 79.88 |
Symmetry | |
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Space Group | P 1 |
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 | 100 | CCD | MARMOSAIC 325 mm CCD | 2018-07-09 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2018-11-16 | M | SINGLE WAVELENGTH | ||||||
3 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2019-02-15 | M | SINGLE WAVELENGTH | ||||||
4 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 9M | 2020-07-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL14-1 | 1.195 | SSRL | BL14-1 |
2 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.9792 | SSRL | BL12-2 |
3 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-2 | 0.9793 | NSLS-II | 17-ID-2 |
4 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-1 | 0.9201 | NSLS-II | 17-ID-1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.89 | 78.64 | 95.9 | 0.061 | 0.063 | 0.015 | 1 | 31.6 | 18.3 | 137673 | 35.12 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.89 | 1.92 | 94 | 1.294 | 1.329 | 0.303 | 0.907 | 2.2 | 19 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.89 | 61.01 | 137668 | 6768 | 95.9 | 0.196 | 0.195 | 0.218 | RANDOM | 48.49 |
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] | |
-2.4352 | 10.4462 | -3.061 | 3.4146 | -1.2604 | -0.9794 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_omega_torsion | 3.46 |
t_other_torsion | 2.8 |
t_angle_deg | 0.99 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10652 |
Nucleic Acid Atoms | |
Solvent Atoms | 1412 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
PDB_EXTRACT | data extraction |
autoPROC | data reduction |
autoPROC | data scaling |
PHENIX | phasing |