3ODS
Crystal structure of the K185A mutant of the N-terminal domain of human Symplekin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 50MM BIS-TRIS, 40MM AMMONIUM SULFATE, 40% (V/V) PENTAERYTHRITOL ETHOXYLATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.83 | 32.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 32.193 | α = 79.45 |
b = 44.039 | β = 80.55 |
c = 63.463 | γ = 73.84 |
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 | ADSC QUANTUM 315r | MIRRORS | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | NSLS | X29A |
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 | 1.9 | 30 | 96.6 | 0.021 | 29.1092 | 2 | 24917 |
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) | |||||||||||
1.9 | 1.97 | 89.9 | 0.09 | 5.739 | 1.9 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.9 | 30 | 23604 | 1265 | 96.6 | 0.17929 | 0.17648 | 0.23076 | RANDOM | 26.659 |
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] | |
2.41 | 0.5 | 1.28 | -1.85 | 0.01 | -1.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.167 |
r_dihedral_angle_4_deg | 23.004 |
r_dihedral_angle_3_deg | 14.825 |
r_scangle_it | 4.945 |
r_dihedral_angle_1_deg | 4.916 |
r_scbond_it | 2.978 |
r_mcangle_it | 1.7 |
r_angle_refined_deg | 1.477 |
r_mcbond_it | 0.897 |
r_chiral_restr | 0.107 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2531 |
Nucleic Acid Atoms | |
Solvent Atoms | 208 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
CBASS | data collection |
COMO | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |