4DRI

Co-crystal structure of the PPIase domain of FKBP51, Rapamycin and the FRB fragment of mTOR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FAPPDB ENTRY 1FAP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.529325% PEG3350, 0.1 M NaCl, 0.1M HEPES-NaOH pH 7.5, vapor diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2144.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.503α = 90
b = 59.554β = 90
c = 67.787γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9788ESRFID29

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
11.4567.78795.70.0430.04317.33.8413154131518.77
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)
11.451.5393.80.3770.37723.55806

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 1FAP1.4519.054127539213206295.160.17840.17840.17690.2064RANDOM25.4582
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]
-0.04-0.040.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.618
r_dihedral_angle_4_deg16.59
r_dihedral_angle_3_deg13.009
r_dihedral_angle_1_deg6.778
r_scangle_it3.471
r_scbond_it2.281
r_angle_refined_deg1.546
r_mcangle_it1.435
r_mcbond_it0.954
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.618
r_dihedral_angle_4_deg16.59
r_dihedral_angle_3_deg13.009
r_dihedral_angle_1_deg6.778
r_scangle_it3.471
r_scbond_it2.281
r_angle_refined_deg1.546
r_mcangle_it1.435
r_mcbond_it0.954
r_nbtor_refined0.312
r_nbd_refined0.209
r_symmetry_vdw_refined0.203
r_xyhbond_nbd_refined0.129
r_chiral_restr0.1
r_symmetry_hbond_refined0.082
r_bond_refined_d0.014
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1718
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms65

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction