1MGW
Crystal structure of RNase Sa3, cytotoxic microbial ribonuclease
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.6 | 293 | Tris, HCl, HEPES, lithium sulphate, pH 7.6, VAPOR DIFFUSION, HANGING DROP at 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.8 | 68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.72 | α = 90 |
b = 64.72 | β = 90 |
c = 69.57 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | IMAGE PLATE | MARRESEARCH | 2000-04-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X31 | 1.100 | EMBL/DESY, Hamburg | X31 |
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 | 2 | 29.6 | 100 | 0.06 | 31.6 | 9.5 | 11799 | 11799 | 28.5 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
2 | 2.02 | 99.5 | 0.306 | 5.8 | 7.9 | 390 |
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 | 1RGG | 2 | 29 | 11799 | 11760 | 559 | 100 | 0.155 | 0.155 | 0.154 | 0.212 | RANDOM | 25.813 |
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] | |
2.09 | 1.05 | 2.09 | -3.14 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 14.373 |
p_scangle_it | 5.842 |
r_scangle_it | 5.842 |
r_dihedral_angle_1_deg | 5.479 |
r_sphericity_bonded | 4.616 |
p_scbond_it | 3.836 |
r_scbond_it | 3.836 |
p_mcangle_it | 2.56 |
r_mcangle_it | 2.56 |
r_rigid_bond_restr | 1.954 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 782 |
Nucleic Acid Atoms | |
Solvent Atoms | 145 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
REFMAC | refinement |