5FCP
X-RAY STRUCTURE OF THE ADDUCT BETWEEN HEN EGG WHITE LYSOZYME AND CISPLATIN AT LONG INCUBATION TIMES
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 193L |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | Crystals were grown using a reservoir solution of 1.1 M NaCl, 0.1 M sodium acetate pH 4.4 and a drop of 1 uL adduct solution and 1 uL reservoir solution. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.28 | α = 90 |
b = 79.28 | β = 90 |
c = 37.45 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 2M | 2015-07-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | 1.0650 | ELETTRA | 5.2R |
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 | 1.55 | 56.06 | 97.6 | 0.095 | 11.9 | 5.7 | 18069 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.55 | 1.58 | 99.1 | 1.005 | 0.273 | 0.8 | 5.8 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 193L | 1.55 | 56.06 | 16465 | 868 | 96.95 | 0.17005 | 0.16787 | 0.21289 | RANDOM | 24.018 |
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] | |
0.12 | 0.12 | -0.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.064 |
r_dihedral_angle_4_deg | 22.43 |
r_dihedral_angle_3_deg | 12.405 |
r_long_range_B_refined | 7.576 |
r_long_range_B_other | 7.268 |
r_dihedral_angle_1_deg | 6.275 |
r_scangle_other | 5.788 |
r_scbond_it | 3.873 |
r_scbond_other | 3.793 |
r_mcangle_other | 2.995 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1001 |
Nucleic Acid Atoms | |
Solvent Atoms | 121 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
REFMAC | phasing |