4RSK
STRUCTURE OF THE K7A/R10A/K66A VARIANT OF RIBONUCLEASE A COMPLEXED WITH 3'-UMP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | CRYSTALS WERE PREPARED USING THE HANGING DROP METHOD. LYOPHILIZED K7A/R10A/K66A RNASE A WAS DISSOLVED IN UNBUFFERED WATER TO A CONCENTRATION OF 60MG/ML. DROPS CONSISTING OF PROTEIN SOLUTION (1.5MICROLITER), WATER (1.5MICROLITER), AND RESERVOIR SOLUTION (3.0MICROLITER) WERE SUSPENDED OVER 0.5 ML OF RESERVOIR SOLUTION (0.1M SODIUM ACETATE BUFFER, PH 4.5, CONTAINING 36% PEG 4000). THE COMPLEX WITH 3'-UMP WAS PREPARED BY SOAKING CRYSTALS IN MOTHER LIQUOR CONTAINING 5MM 3'-UMP FOR 2 DAYS., vapor diffusion - hanging drop |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.47 | 60 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.62 | α = 90 |
b = 69.62 | β = 90 |
c = 66.98 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 | 273 | AREA DETECTOR | SIEMENS | LONG MIRRORS | 1997-09-12 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH2R |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 30 | 88 | 0.026 | 19.8 | 2.4 | 33552 | 0.33 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.1 | 2.2 | 88 | 0.12 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | DIFFERENCE FOURIER | PDB ENTRY 3RSK | 2.1 | 30 | 14210 | 14210 | 88 | 0.168 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_dihedral_angle_d | 17.475 |
t_angle_deg | 2.208 |
t_it | 1 |
t_nbd | 0.018 |
t_bond_d | 0.011 |
t_gen_planes | 0.011 |
t_trig_c_planes | 0.006 |
t_incorr_chiral_ct | |
t_pseud_angle |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 937 |
Nucleic Acid Atoms | |
Solvent Atoms | 94 |
Heterogen Atoms | 21 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
XCALIBRE | data reduction |
TNT | refinement |
XDS | data reduction |
XCALIBRE | data scaling |
TNT | phasing |