3KEV
X-ray crystal structure of a DCUN1 domain-containing protein from Galdieria sulfuraria
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 293 | 30% PEG 1500, 100 mM sodium acetate pH 5.0, 150 mM MgCl2, 50 mM NaCl, 5 mM HEPES pH 7.0, 0.3 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
2 | VAPOR DIFFUSION, SITTING DROP | 5 | 293 | 27% PEG 1500, 100 mM sodium acetate pH 5.0, 150 mM LiCl2, 50 mM NaCl, 5 mM HEPES pH 7.0, 0.3 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.743 | α = 90 |
b = 52.422 | β = 111.17 |
c = 49.113 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 300 mm CCD | 2009-10-12 | SINGLE WAVELENGTH | |||||||
2 | 2 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | 2009-10-18 | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | .97625 | APS | 21-ID-D |
2 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.96426, 0.97949, 0.97965, 0.99522 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.3 | 50 | 98.5 | 0.04 | 16 | 4 | 42886 | 42243 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1,2 | 1.3 | 1.32 | 87.2 | 0.388 | 2.6 | 3 | 1849 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MAD, MR | 1.3 | 20.984 | 1.35 | 42820 | 42161 | 2111 | 98.46 | 0.156 | 0.156 | 0.155 | 0.178 | random | 20.012 |
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] | |
-1.285 | 2.593 | -2.06 | 3.345 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.426 |
f_angle_d | 1.566 |
f_chiral_restr | 0.101 |
f_bond_d | 0.018 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1525 |
Nucleic Acid Atoms | |
Solvent Atoms | 176 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
SHARP | phasing |
DM | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data scaling |