4DRN

EVALUATION OF SYNTHETIC FK506 ANALOGS AS LIGANDS FOR FKBP51 AND FKBP52: COMPLEX OF FKBP51 WITH {3-[(1R)-3-(3,4-dimethoxyphenyl)-1-({[(2S)-1-{[(1S,2R)-2-ethyl-1-hydroxycyclohexyl](oxo)acetyl}piperidin-2-yl]carbonyl}oxy)propyl]phenoxy}acetic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3O5Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.529337.5 % PEG3350, 0.1 M NH4OAc, 0.1 M HEPES pH 7.5, 10 % DMSO, vapor diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6353.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.27α = 90
b = 52.537β = 90
c = 57.018γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.900ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.06925.05795.20.0450.04513.23.762752627528.05
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.071.1391.40.5760.5761.43.78686

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3O5Q1.069206269059549314194.930.15570.15570.15480.1724RANDOM13.5351
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]
0.30.32-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.465
r_dihedral_angle_4_deg12.197
r_dihedral_angle_3_deg9.711
r_dihedral_angle_1_deg7.18
r_sphericity_free5.866
r_scangle_it3.352
r_sphericity_bonded3.12
r_scbond_it2.56
r_mcangle_it1.802
r_angle_refined_deg1.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.465
r_dihedral_angle_4_deg12.197
r_dihedral_angle_3_deg9.711
r_dihedral_angle_1_deg7.18
r_sphericity_free5.866
r_scangle_it3.352
r_sphericity_bonded3.12
r_scbond_it2.56
r_mcangle_it1.802
r_angle_refined_deg1.6
r_mcbond_it1.416
r_rigid_bond_restr1.38
r_angle_other_deg0.856
r_mcbond_other0.543
r_symmetry_vdw_refined0.343
r_symmetry_vdw_other0.286
r_nbd_refined0.233
r_nbd_other0.206
r_xyhbond_nbd_refined0.184
r_nbtor_refined0.182
r_symmetry_hbond_refined0.098
r_nbtor_other0.097
r_chiral_restr0.092
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms980
Nucleic Acid Atoms
Solvent Atoms284
Heterogen Atoms46

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling