1KM9
The Structure of a Cytotoxic Ribonuclease From the Oocyte of Rana Catesbeiana (Bullfrog)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1RCA | PDB ENTRY 1RCA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 298 | PEG 4000, ammonium phosphate, NaOAc, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.806 | α = 90 |
b = 45.918 | β = 90 |
c = 57.459 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 115 | IMAGE PLATE | RIGAKU RAXIS IIC | mirrors | 1998-02-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU300 | 1.5418 |
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 | 1.96 | 24.36 | 94.2 | 0.055 | 9.4 | 5.62 | 8085 | 8085 | 17.7 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1.95 | 1.98 | 91.8 | 0.196 | 7.06 | 4.2 | 402 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1RCA | 1.96 | 24.36 | 8607 | 7970 | 672 | 92.6 | 0.181 | 0.181 | 0.178 | 0.216 | RANDOM | 29.53 |
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] | |
-6.82 | 10.91 | -4.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 25.2 |
x_angle_deg | 1.8 |
x_improper_angle_d | 1.22 |
x_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 864 |
Nucleic Acid Atoms | |
Solvent Atoms | 108 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
SCALEPACK | data scaling |
CNS | phasing |