7NQB
X.ray structure of the oxaliplatin/beta-lactoglobulin adduct
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 0.2M KCl, 0.04M HEPES, 35% v/v pentaerythritol propoxylate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.86 | 33.91 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 35.87 | α = 90 |
b = 112.58 | β = 117.637 |
c = 38.08 | 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 | 100 | PIXEL | DECTRIS PILATUS 6M | 2020-11-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 11.2C | 0.96 | ELETTRA | 11.2C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 2.01 | 56.3 | 86.9 | 0.06 | 0.958 | 8.8 | 2.3 | 17918 | 19.3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.01 | 56.3 | 92.4 | 0.152 | 0.939 | 3.9 | 1.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6ZSR | 2.01 | 56.3 | 17379 | 772 | 97.635 | 0.216 | 0.2123 | 0.2845 | 24.961 |
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] | |
-0.105 | -0.076 | 0.054 | 0.085 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.574 |
r_dihedral_angle_3_deg | 18.696 |
r_dihedral_angle_4_deg | 8.786 |
r_dihedral_angle_1_deg | 7.398 |
r_lrange_it | 6.122 |
r_lrange_other | 6.122 |
r_scangle_it | 4.093 |
r_scangle_other | 4.092 |
r_mcangle_it | 3.337 |
r_mcangle_other | 3.337 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2521 |
Nucleic Acid Atoms | |
Solvent Atoms | 64 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
MOSFLM | data scaling |
PHASER | phasing |