6I6U
Circular permutant of ribosomal protein S6, adding 9aa to N terminal of P81-82, L75A mutant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1RIS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M Calcium chloride dehydrate 0.1 M Tris pH 8.0 20% w/v PEG 6000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.84 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 72.91 | α = 90 |
b = 43.92 | β = 117.18 |
c = 70.63 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | PIXEL | DECTRIS EIGER X 16M | 2018-01-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX IV BEAMLINE BioMAX | 0.97999 | MAX IV | BioMAX |
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 | 1.57 | 62.83 | 99.9 | 0.071 | 0.077 | 0.03 | 0.998 | 11.9 | 6.7 | 28101 |
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 | 1.57 | 1.59 | 100 | 0.943 | 1.022 | 0.39 | 0.772 | 6.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 1Ris | 1.57 | 62.83 | 26699 | 1409 | 99.8 | 0.2103 | 0.2079 | 0.2563 | RANDOM | 33.166 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.12 | -0.7 | 2.35 | -0.99 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.048 |
r_dihedral_angle_4_deg | 17.94 |
r_dihedral_angle_3_deg | 15.553 |
r_dihedral_angle_1_deg | 6.285 |
r_angle_refined_deg | 2.121 |
r_angle_other_deg | 1.134 |
r_chiral_restr | 0.123 |
r_bond_refined_d | 0.02 |
r_gen_planes_refined | 0.01 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1683 |
Nucleic Acid Atoms | |
Solvent Atoms | 100 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
MOLREP | phasing |