5DIU
The Fk1 domain of FKBP51 in complex with the new synthetic ligand 2-(3-((R)-1-((S)-1-((S)-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)acetyl)piperidine-2-carboxamido)-3-(3,4-dimethoxyphenyl)propyl)phenoxy)acetic acid
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 | 10 % 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 |
2.21 | 44.27 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 45.029 | α = 90 |
b = 48.414 | β = 90 |
c = 56.852 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 2012-12-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.03679 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.301 | 48.414 | 99.5 | 0.053 | 0.06 | 0.02 | 15.7 | 8.3 | 31101 | 31101 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.3 | 1.37 | 97 | 1.043 | 1.043 | 0.431 | 0.7 | 7.4 | 4327 |
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 | 3o5q | 1.3 | 30 | 29490 | 1550 | 99.56 | 0.1462 | 0.1441 | 0.1852 | RANDOM | 21.323 |
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] | |
1.16 | -0.83 | -0.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 30.975 |
r_dihedral_angle_2_deg | 27.451 |
r_dihedral_angle_3_deg | 15.054 |
r_sphericity_bonded | 11.681 |
r_dihedral_angle_1_deg | 8.575 |
r_dihedral_angle_4_deg | 7.997 |
r_rigid_bond_restr | 6.089 |
r_angle_refined_deg | 2.374 |
r_angle_other_deg | 1.11 |
r_chiral_restr | 0.143 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 968 |
Nucleic Acid Atoms | |
Solvent Atoms | 141 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |
XDS | data reduction |