3KFD | pdb_00003kfd

Ternary complex of TGF-b1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2TGIPDB entries 2TGI, 1M9Z, 1REW
experimental modelPDB 1M9ZPDB entries 2TGI, 1M9Z, 1REW
experimental modelPDB 1REWPDB entries 2TGI, 1M9Z, 1REW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72988-15% Peg 4000-8000, pH 7.0, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4349.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.7α = 64.01
b = 99.35β = 84.47
c = 102.7γ = 84.34
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2007-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13500.089.21.923426-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
33.110.24521.61223

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB entries 2TGI, 1M9Z, 1REW2.99546.080.0622125106282.550.220.2170.210.2680.26Random73.45
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]
3.635-2.7280.206-6.6628.384-31.29
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d20.035
f_angle_d0.631
f_chiral_restr0.044
f_bond_d0.003
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9058
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms

Software

Software
Software NamePurpose
PHASERphasing
EPMRphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling