4S0Q
The X-ray structure of the adduct formed in the reaction between bovine pancreatic ribonuclease and carboplatin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 298 | Crystals of the RNase A-carboplatin adduct have been obtained by soaking experiments where pre-grown monoclinic protein crystals were incubated with an excess of the platinum drug (at a protein to platinum ratio 1:10). Crystals of RNase A were grown by hanging-drop vapor mixing 1 L of RNase A at 20 mg mL-1 with equal volumes of reservoir solution containing 20% PEG4000 and 20 mM sodium citrate buffer pH 5.0 at 298 K. Two weeks after their appearance, crystals were soaked for four days in a solution of Carboplatin dissolved in 10 L of reservoir. At the final, Pt drug:protein concentrations were in 10:1 ratio., VAPOR DIFFUSION, HANGING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.521 | α = 90 |
b = 32.499 | β = 89.59 |
c = 72.711 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 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 | 2.09 | 72.71 | 99.7 | 0.124 | 5.6 | 14095 | 14095 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 code 1JVT, chain A without water molecules and ligands | 2.09 | 72.71 | 13380 | 13380 | 709 | 99.02 | 0.20801 | 0.20801 | 0.20518 | 0.26175 | RANDOM | 37.837 |
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] | |
-1.17 | -0.16 | 0.48 | 0.68 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.511 |
r_dihedral_angle_3_deg | 15.188 |
r_dihedral_angle_4_deg | 10.612 |
r_dihedral_angle_1_deg | 6.895 |
r_long_range_B_refined | 6.465 |
r_long_range_B_other | 6.454 |
r_scangle_other | 4.656 |
r_mcangle_it | 3.991 |
r_mcangle_other | 3.99 |
r_scbond_it | 3.219 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1844 |
Nucleic Acid Atoms | |
Solvent Atoms | 104 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |