4G4B
Room temperature X-ray diffraction study of cisplatin binding to HEWL in DMSO media with NAG after 7 months of crystal storage
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2W1Y | PDB ENTRY 2W1Y |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH | 4.7 | 295 | HEWL co-crystallized with cisplatin and NAG in 7.5% DMSO media in 1 mL 10% sodium chloride + 1 ml 0.04 M sodium acetate, pH 4.7, BATCH, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.822 | α = 90 |
b = 78.822 | β = 90 |
c = 38.019 | 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 | 295 | CCD | APEX II CCD | 2012-01-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 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 | 2.1 | 55.736 | 52.6 | 0.177 | 16.1 | 19.2 | 13385 | 7055 | 4 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.1 | 2.13 | 100 | 0.749 | 5.1 | 13.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | 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 | PDB ENTRY 2W1Y | 2.1 | 55.736 | 2 | 4 | 13385 | 7050 | 343 | 99.99 | 0.16233 | 0.15927 | 0.22701 | RANDOM | 24.044 |
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] | |
-0.1 | -0.1 | 0.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.27 |
r_dihedral_angle_4_deg | 25.586 |
r_dihedral_angle_3_deg | 15.313 |
r_dihedral_angle_1_deg | 7.096 |
r_angle_refined_deg | 2.531 |
r_angle_other_deg | 1.07 |
r_chiral_restr | 0.118 |
r_bond_refined_d | 0.018 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1001 |
Nucleic Acid Atoms | |
Solvent Atoms | 35 |
Heterogen Atoms | 29 |
Software
Software | |
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Software Name | Purpose |
APEX | data collection |
PHASER | phasing |
REFMAC | refinement |
EVAL15 | data reduction |
EVAL15 | data scaling |