6GQ6
Structure of human Heat shock protein 90-alpha N-terminal domain (Hsp90-NTD) in complex with ADP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2XK2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | Precipitant: 25 % wt/vol PEG 2000, 200mM MgCl2, 100 mM sodium cacodylate, pH 6.5 Sample: Hsp90a-NTD 20 mg/mL, 10 mM ADP, 500 mM NaCl, 20 mM TRIS, pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.87 | 34.18 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 53.256 | ¦Á = 90 |
b = 42.214 | ¦Â = 115.98 |
c = 54.002 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 PILATUS3 6M | 2017-02-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.96861 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.25 | 45.47 | 97.1 | 0.099 | 0.122 | 0.07 | 0.992 | 6.9 | 2.8 | 10124 | 2 | 26.6 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.25 | 2.37 | 98.5 | 0.424 | 0.523 | 0.302 | 0.74 | 2.8 | 2.8 |
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 | 2XK2 | 2.25 | 31.87 | 9623 | 489 | 96.8 | 0.17609 | 0.17294 | 0.2368 | RANDOM | 25.421 |
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] | |
-0.13 | -0.02 | 0.02 | 0.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.962 |
r_dihedral_angle_4_deg | 27.89 |
r_dihedral_angle_3_deg | 18.119 |
r_dihedral_angle_1_deg | 7.395 |
r_long_range_B_refined | 6.108 |
r_mcangle_it | 3.12 |
r_scbond_it | 2.396 |
r_angle_refined_deg | 2.083 |
r_mcbond_it | 1.928 |
r_chiral_restr | 0.133 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1612 |
Nucleic Acid Atoms | |
Solvent Atoms | 130 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |