4W9O
The Fk1 domain of FKBP51 in complex with (1S,5S,6R)-10-[(3,5-dichlorophenyl)sulfonyl]-5-[(1R)-1,2-dihydroxyethyl]-3-[2-(3,4-dimethoxyphenoxy)ethyl]-3,10-diazabicyclo[4.3.1]decan-2-one
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3O5Q |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 34 % PEG-3350, 0.2 M NH4-acetate and 0.1 M HEPES-NaOH pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 72.704 | α = 90 |
b = 50.586 | β = 115.54 |
c = 68.953 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2013-04-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.97949 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.27 | 40.06 | 99.3 | 0.061 | 0.036 | 0.999 | 10.5 | 3.7 | 59102 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.27 | 1.29 | 96.1 | 0.636 | 0.385 | 0.636 | 1.9 | 3.6 | 2815 |
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 | 3O5Q | 1.27 | 30 | 56123 | 2979 | 99.17 | 0.1413 | 0.1393 | 0.1775 | RANDOM | 14.999 |
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] | |
1.26 | -0.24 | -0.59 | -0.39 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.225 |
r_sphericity_free | 20.626 |
r_dihedral_angle_3_deg | 11.476 |
r_dihedral_angle_4_deg | 11.26 |
r_dihedral_angle_1_deg | 6.765 |
r_sphericity_bonded | 6.212 |
r_rigid_bond_restr | 3.179 |
r_angle_refined_deg | 1.526 |
r_angle_other_deg | 0.891 |
r_chiral_restr | 0.124 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1927 |
Nucleic Acid Atoms | |
Solvent Atoms | 305 |
Heterogen Atoms | 86 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |
XDS | data reduction |
XSCALE | data reduction |