4E0K

Crystal Structure of the amyloid-fibril forming peptide KDWSFY derived from human Beta 2 Microglobulin (58-63)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52900.1M BIS-TRIS PROPANE pH 6.5, 0.2 M SODIUM FLUORIDE, 20% (w/v) PEG 3350, vapor diffusion, hanging drop, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
1.9536.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.37α = 90
b = 62.37β = 90
c = 11.73γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97911APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
10.9714.98199.30.06912.66-39.162
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.97197.40.4482.42

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONSIRAS0.9714.9812.0115997160199.840.11380.11190.131110.9748
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]
0.22070.2207-0.4415
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d19.613
f_angle_d1.417
f_chiral_restr0.095
f_bond_d0.01
f_plane_restr0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms244
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms31

Software

Software
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction