5GS9
Crystal structure of CASTOR1-arginine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 289 | 0.1M sodium citrate (pH 5.0), 20% (w/v) PEG 8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.644 | α = 90 |
b = 83.564 | β = 116.61 |
c = 97.81 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CMOS | DECTRIS PILATUS3 S 6M | 2016-07-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL19U1 | 0.9785 | SSRF | BL19U1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.5 | 50.01 | 99.9 | 0.085 | 4 | 6.7 | 47062 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.5 | 2.59 | 99.7 | 0.495 | 0.872 | 6.2 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.5 | 50.01 | 44415 | 2360 | 99.68 | 0.1778 | 0.1754 | 0.2238 | RANDOM | 52.176 |
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] | |
-0.62 | -1.05 | 1.11 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 34.63 |
r_dihedral_angle_2_deg | 32.962 |
r_sphericity_bonded | 23.185 |
r_dihedral_angle_3_deg | 14.619 |
r_dihedral_angle_4_deg | 14.132 |
r_dihedral_angle_1_deg | 6.144 |
r_mcangle_it | 1.705 |
r_scbond_it | 1.413 |
r_mcbond_it | 1.292 |
r_angle_refined_deg | 1.255 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9249 |
Nucleic Acid Atoms | |
Solvent Atoms | 314 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
HKL-3000 | data collection |
HKL-3000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |