3MNR
Crystal Structure of Benzamide SNX-1321 bound to Hsp90
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIQUID DIFFUSION | 6.5 | 277 | Crystallized in 0.2M MgCl2, 0.1M Bis-Tris pH 6.5, and 20% PEG 3350 and were cryo-protected by adding 25% Ethylene Glycol to the mother liquor and passing the crystal through the solution immediately before flash freezing it in liquid nitrogen. The drops were setup by hand, adding 0.5ul protein to 0.5ul of reservoir in a sitting drop 192-well corning crystallization plate and incubated at 277K. , LIQUID DIFFUSION |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.87 | 57.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.773 | α = 90 |
b = 90.753 | β = 90 |
c = 99.116 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 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 | 113.5 | CCD | RIGAKU SATURN 92 | 2004-10-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.9 | 36.45 | 95 | 0.084 | 10.8 | 2.74 | 23062 | 21887 | 3 | 10.8 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.9 | 1.97 | 95 | 0.13 | 1.8 | 1.8 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3D0B | 1.9 | 36.45 | 23062 | 21887 | 1175 | 95.56 | 0.19021 | 0.18784 | 0.23458 | RANDOM | 20.528 |
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] | |
-0.24 | 0.7 | -0.46 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.964 |
r_dihedral_angle_4_deg | 20.326 |
r_dihedral_angle_3_deg | 12.74 |
r_dihedral_angle_1_deg | 5.831 |
r_scangle_it | 2.59 |
r_scbond_it | 1.589 |
r_angle_refined_deg | 1.302 |
r_mcangle_it | 1.111 |
r_mcbond_it | 0.671 |
r_nbtor_refined | 0.301 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1644 |
Nucleic Acid Atoms | |
Solvent Atoms | 345 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |