5YH1
Member of s1p family of ribosomal proteins PF0399 DHH domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 4% (V/V) PEG 400 100 mM Sodium acetate/ Acetic acid pH 5.5 2000 mM Lithium sulfate 100 mM Magnesium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.31 | 76.84 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 132.5 | α = 90 |
b = 132.5 | β = 90 |
c = 212.245 | γ = 120 |
Symmetry | |
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Space Group | P 63 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2015-09-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NFPSS BEAMLINE BL19U1 | 0.9785 | NFPSS | BL19U1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.18 | 50 | 97 | 15 | 33.6 | 56239 |
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 | THROUGHOUT | 2.18 | 25.25 | 48383 | 2583 | 87.9 | 0.187 | 0.187 | 0.202 | RANDOM | 34.78 |
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] | |
0.02 | 0.02 | 0.02 | -0.08 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.762 |
r_dihedral_angle_4_deg | 16.225 |
r_dihedral_angle_3_deg | 13.856 |
r_long_range_B_refined | 5.176 |
r_long_range_B_other | 5.175 |
r_dihedral_angle_1_deg | 5.06 |
r_scangle_other | 3.498 |
r_mcangle_it | 2.237 |
r_mcangle_other | 2.237 |
r_scbond_it | 2.178 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3503 |
Nucleic Acid Atoms | |
Solvent Atoms | 159 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Coot | model building |
AutoSol | phasing |
HKL-3000 | data processing |