6GHX

Alzheimer's Amyloid-Beta Peptide Fragment 31-35 in Complex with Cd-substituted Thermolysin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KEIpdbid 1kei

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION629350 mM MES: 45% DMSO: 0.7-0.9 M NaCl: 0-0.4 M CdCl2: reservoir solution containing 30-40% ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.3547.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.06α = 90
b = 93.06β = 90
c = 130.29γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-FBe CRL lenses for vertical focusing and Rh/Pt/Si coated ellipitcal mirror for horizontal focusing2018-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.07227ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.1646.531000.0720.0740.0170.99917.217.311487217.97
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.161.21002.7852.8740.7030.46516.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdbid 1kei1.15646.531.35115073574499.190.20250.20160.219823.7965
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d2.78
f_angle_d0.824
f_chiral_restr0.081
f_bond_d0.005
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2448
Nucleic Acid Atoms
Solvent Atoms367
Heterogen Atoms25

Software

Software
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing