4GCB
100K X-ray diffraction study of a 6-fold molar excess of a cisplatin/carboplatin mixture binding to HEWL
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.7 | 277 | 49 mg HEWL (3.2 mM), 3 mg cisplatin (10 mM), 3.7 mg carboplatin (10 mM) in 0.04 M sodium acetate buffer (462.5 uL) + 10% sodium chloride precipitant (462.5 uL) + 1 mM DMSO (75 uL), pH 4.7, BATCH, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.99 | 38.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.78 | α = 90 |
b = 78.78 | β = 90 |
c = 36.987 | 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 | CCD | Bruker Platinum 135 | Incoatec Helios confocal optics | 2012-05-23 | 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 | 1.8 | 55.71 | 100 | 0.069 | 78.8 | 113.6 | 10718 | 10718 | 4 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.8 | 1.85 | 99 | 0.305 | 14.3 | 44.2 |
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 | 1.8 | 55.71 | 2 | 4 | 10718 | 10718 | 536 | 99.76 | 0.17617 | 0.17445 | 0.2096 | RANDOM | 11.778 |
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] | |
0.23 | 0.23 | -0.45 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.125 |
r_dihedral_angle_4_deg | 18.565 |
r_dihedral_angle_3_deg | 14.272 |
r_dihedral_angle_1_deg | 6.487 |
r_angle_refined_deg | 2.153 |
r_angle_other_deg | 1.148 |
r_chiral_restr | 0.135 |
r_bond_refined_d | 0.019 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1001 |
Nucleic Acid Atoms | |
Solvent Atoms | 107 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
PROTEUM PLUS | data collection |
PHASER | phasing |
REFMAC | refinement |
PROTEUM PLUS | data reduction |
PROTEUM PLUS | data scaling |