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)
TypeSourceAccession CodeDetails
experimental modelPDB 3O5Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529310 % PEG-3350, 0.2 M NH4-acetate and 0.1 M HEPES-NaOH pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.2144.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.029α = 90
b = 48.414β = 90
c = 56.852γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.03679SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.30148.41499.50.0530.060.0215.78.33110131101
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)RedundancyNumber Unique Reflections (All)
11.31.37971.0431.0430.4310.77.44327

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3o5q1.33029490155099.560.14620.14410.1852RANDOM21.323
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
KeyRefinement Restraint Deviation
r_sphericity_free30.975
r_dihedral_angle_2_deg27.451
r_dihedral_angle_3_deg15.054
r_sphericity_bonded11.681
r_dihedral_angle_1_deg8.575
r_dihedral_angle_4_deg7.997
r_rigid_bond_restr6.089
r_angle_refined_deg2.374
r_angle_other_deg1.11
r_chiral_restr0.143
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free30.975
r_dihedral_angle_2_deg27.451
r_dihedral_angle_3_deg15.054
r_sphericity_bonded11.681
r_dihedral_angle_1_deg8.575
r_dihedral_angle_4_deg7.997
r_rigid_bond_restr6.089
r_angle_refined_deg2.374
r_angle_other_deg1.11
r_chiral_restr0.143
r_bond_refined_d0.025
r_gen_planes_refined0.012
r_bond_other_d0.005
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms968
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction