3T1W

Structure of the four-domain fragment Fn7B89 of oncofetal fibronectin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FNF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP929326 %(w/v) PEG3350, 0.1 M Tris-HCl, 0.2 M NaCl, 5 %(v/v) Isopropanol, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8857.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 211.98α = 90
b = 29.115β = 111.42
c = 82.241γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDdouble crystal2009-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

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
12.43099.50.05618.83.71903418943-3-344.1
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)
12.42.599.70.4253.53.72147

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1FNF2.4302179661796697699.760.230080.227550.27693RANDOM59.608
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]
-1.98-0.412.18-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.466
r_dihedral_angle_4_deg18.446
r_dihedral_angle_3_deg15.04
r_dihedral_angle_1_deg6.297
r_scangle_it2.935
r_scbond_it1.628
r_angle_refined_deg1.15
r_mcangle_it0.828
r_mcbond_it0.419
r_chiral_restr0.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.466
r_dihedral_angle_4_deg18.446
r_dihedral_angle_3_deg15.04
r_dihedral_angle_1_deg6.297
r_scangle_it2.935
r_scbond_it1.628
r_angle_refined_deg1.15
r_mcangle_it0.828
r_mcbond_it0.419
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2821
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling