1M07
RESIDUES INVOLVED IN THE CATALYSIS AND BASE SPECIFICITY OF CYTOTOXIC RIBONUCLEASE FROM BULLFROG (RANA CATESBEIANA)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 298 | 0.1 M potassium sodium tartrate tetrahydrate, 24 % PEG 8000, 0.05 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 38.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 28.629 | α = 90 |
b = 53.566 | β = 98.31 |
c = 72.203 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 298 | CCD | ADSC QUANTUM 4 | KOHZU double crystal monochromator | 2000-08-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | 1.05 | NSLS | X4A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.79 | 19.68 | 90.1 | 0.073 | 0.073 | 11.1 | 6.81 | 20226 | 18075 | 14.8 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.8 | 1.83 | 90.5 | 0.18 | 0.18 | 6.2 | 2.1 | 894 |
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 1KM8 | 1.8 | 19.68 | 20134 | 17518 | 1369 | 87 | 0.227 | 0.227 | 0.189 | 0.228 | RANDOM | 25.29 |
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] | |
15.03 | 2.85 | -7.76 | -7.27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_torsion_deg | 26.4 |
x_dihedral_angle_d | 26.4 |
x_torsion_impr_deg | 4.3 |
x_improper_angle_d | 4.3 |
x_scangle_it | 3.14 |
x_angle_deg | 2.5 |
x_scbond_it | 2.09 |
x_mcangle_it | 1.84 |
x_mcbond_it | 1.27 |
x_bond_d | 0.016 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1736 |
Nucleic Acid Atoms | 160 |
Solvent Atoms | 323 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
ADSC | data collection |
SCALEPACK | data scaling |
CNS | phasing |