3RSK
STRUCTURE OF THE K7A/R10A/K66A VARIANT OF RIBONUCLEASE A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1RPH | PDB ENTRY 1RPH |
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 (1.5UL), WATER (1.5UL), AND RESERVOIR SOLUTION (3.0UL) WERE SUSPENDED OVER 0.5 ML OF RESERVOIR SOLUTION [0.1M SODIUM ACETATE BUFFER, PH 4.5, CONTAINING 36% PEG 4000., vapor diffusion - hanging drop |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.25 | 60 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.15 | α = 90 |
b = 68.15 | β = 90 |
c = 65.51 | 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 | 1997-09-11 | M |
Radiation Source | |||||
---|---|---|---|---|---|
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 | 30 | 91 | 0.023 | 20 | 2.3 | 33804 | 0.33 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.1 | 84 | 0.17 |
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 | MOLECULAR REPLACEMENT | PDB ENTRY 1RPH | 2 | 30 | 14929 | 14929 | 91 | 0.174 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_dihedral_angle_d | 17.868 |
t_angle_deg | 2.236 |
t_it | 1 |
t_nbd | 0.027 |
t_bond_d | 0.01 |
t_gen_planes | 0.01 |
t_trig_c_planes | 0.005 |
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 | 82 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
XCALIBRE | data reduction |
AMoRE | phasing |
TNT | refinement |
XDS | data reduction |
XCALIBRE | data scaling |