2GEE

Crystal Structure of Human Type III Fibronectin Extradomain B and Domain 8


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FNFfragment of Repeat domain 8 from 1fnf

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829810% (w/v) PEG-3350 and 0.2 mM ammonium citrate. , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1939.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.407α = 90
b = 55.288β = 90
c = 74.903γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IV2005-01-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.0128.3699.60.082125532215.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.012.1398.5

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 REPLACEMENTTHROUGHOUTfragment of Repeat domain 8 from 1fnf2.0128.361255312512129199.60.2490.2490.2490.301RANDOM39.7
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]
13.43-10.62-2.82
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d26.9
c_scangle_it3.44
c_mcangle_it2.73
c_scbond_it2.42
c_angle_deg1.9
c_mcbond_it1.74
c_improper_angle_d1.21
c_bond_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1443
Nucleic Acid Atoms
Solvent Atoms384
Heterogen Atoms

Software

Software
Software NamePurpose
CNSrefinement
CrystalCleardata reduction
HKL-2000data scaling
AMoREphasing