4RSZ
The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1HRC | PDB code 1HRC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 300 | A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 120.344 | α = 90 |
b = 120.344 | β = 90 |
c = 36.673 | γ = 120 |
Symmetry | |
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Space Group | P 3 |
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 | CCD | RIGAKU SATURN 944 | mirrors | 2014-07-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | ENRAF-NONIUS FR571 | 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 | 2.19 | 104.22 | 99.8 | 0.109 | 10.4 | 30538 | 30538 |
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 code 1HRC | 2.19 | 104.22 | 28987 | 28987 | 1544 | 99.79 | 0.23403 | 0.23403 | 0.23144 | 0.28211 | RANDOM | 48.561 |
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] | |
-0.8 | -0.4 | -0.8 | 2.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.76 |
r_dihedral_angle_4_deg | 28.912 |
r_dihedral_angle_3_deg | 17.446 |
r_long_range_B_refined | 5.884 |
r_dihedral_angle_1_deg | 5.865 |
r_long_range_B_other | 5.848 |
r_scangle_other | 3.102 |
r_mcangle_it | 2.688 |
r_mcangle_other | 2.687 |
r_scbond_it | 2.276 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4938 |
Nucleic Acid Atoms | |
Solvent Atoms | 127 |
Heterogen Atoms | 347 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |