4OT4
X-ray Structure of the Adduct formed between cisplatin and Ribonuclease A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1JVT | PDB code 1JVT |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 298 | Crystals of RNase A were grown by hanging-drop vapor diffusion technique at 298 K mixing a protein solution containing 20 mg mL-1 of RNase A with equal volumes of reservoir solution. Well diffracting crystals appeared within 15days from the following conditions:20% PEG4000 and 20 mM sodium citrate buffer pH 5.0. , VAPOR DIFFUSION, HANGING DROP |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
1.99 | 38.28 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 99.767 | α = 90 |
b = 32.463 | β = 93.07 |
c = 67.575 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | 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 | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.85 | 50 | 17075 | 17075 |
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 | 1.85 | 30.88 | 16195 | 16195 | 880 | 91.12 | 0.192 | 0.19235 | 0.18924 | 0.24709 | RANDOM | 27.794 |
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] | |
0.03 | 0.24 | 0.82 | -0.85 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.309 |
r_dihedral_angle_4_deg | 17.15 |
r_dihedral_angle_3_deg | 13.064 |
r_dihedral_angle_1_deg | 8.582 |
r_long_range_B_other | 8.194 |
r_long_range_B_refined | 8.161 |
r_mcangle_it | 4.378 |
r_mcangle_other | 4.376 |
r_scangle_other | 4.235 |
r_mcbond_other | 2.814 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1851 |
Nucleic Acid Atoms | |
Solvent Atoms | 125 |
Heterogen Atoms | 8 |
Software
Software | |
---|---|
Software Name | Purpose |
CrystalClear | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |