4DRP

Evaluation of Synthetic FK506 Analogs as Ligands for the FK506-Binding Proteins 51 and 52: Complex of FKBP51 with 2-(3-((R)-3-(3,4-dimethoxyphenyl)-1-((S)-1-(2-((1R,2S)-2-ethyl-1-hydroxy-cyclohexyl)-2-oxoacetyl)piperidine-2-carbonyloxy)propyl)phenoxy)acetic acid from cocrystallization


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3O5QPDB ENTRY 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
2.957.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.913α = 90
b = 56.563β = 90
c = 57.589γ = 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
11.79225.38697.50.0620.06212.43.3154481544820.88
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)
11.791.89840.190.193.92.31862

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3O5Q1.820148531455976998.020.22210.22210.220.2609RANDOM20.0242
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]
0.14-0.09-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.48
r_dihedral_angle_4_deg18.585
r_dihedral_angle_3_deg11.543
r_dihedral_angle_1_deg6.547
r_scangle_it2.927
r_scbond_it1.876
r_angle_refined_deg1.472
r_mcangle_it1.164
r_mcbond_it0.68
r_chiral_restr0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.48
r_dihedral_angle_4_deg18.585
r_dihedral_angle_3_deg11.543
r_dihedral_angle_1_deg6.547
r_scangle_it2.927
r_scbond_it1.876
r_angle_refined_deg1.472
r_mcangle_it1.164
r_mcbond_it0.68
r_chiral_restr0.1
r_bond_refined_d0.013
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms986
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms46

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling