5J86
Crystal Structure of Hsp90-alpha N-domain in complex with 2,4-Dihydroxy-N-methyl-5-(5-oxo-4-o-tolyl-4,5-dihydro-1H-[1,2,4]triazol-3-yl)-N-thiophen-2-ylmethyl-benzamide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1YES |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 277.15 | 0.2 M sodium fluoride, 0.1 M Bis Tris propane, pH 8.5, 20 % w/v PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.19 | 61.45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.078 | α = 90 |
b = 90.24 | β = 90 |
c = 98.089 | 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 | 100 | PIXEL | DECTRIS PILATUS 6M | 2015-09-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.0 | SLS | X10SA |
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 | 1.87 | 36.26 | 99.9 | 0.057 | 14.31 | 6.61 | 24957 | 56.16 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.87 | 1.98 | 99.4 | 0.77 | 6.76 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1YES | 1.87 | 36.26 | 24957 | 1248 | 99.9 | 0.206 | 0.205 | 0.229 | RANDOM | 64.19 |
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] | |
1.2684 | -1.7669 | 0.4985 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 16.27 |
t_omega_torsion | 3.03 |
t_angle_deg | 1.08 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1636 |
Nucleic Acid Atoms | |
Solvent Atoms | 91 |
Heterogen Atoms | 31 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |