3BAE

Crystal structure of Fab WO2 bound to the N terminal domain of Amyloid beta peptide (1-28)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9295100mM bicine, 200mM MgCl2, 20% w/v PEG 8000 , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.8131.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.658α = 90
b = 66.365β = 90
c = 115.337γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++cappilary optics2005-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.5920.38399.70.07311.44.495341653254
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)
1.5931.6341000.033.83.023785

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1PLG1.59320.385341650573268199.70.208970.20680.24968RANDOM11.853
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
r_dihedral_angle_2_deg30.227
r_dihedral_angle_4_deg21.704
r_dihedral_angle_3_deg13.392
r_dihedral_angle_1_deg6.819
r_scangle_it2.944
r_scbond_it2.241
r_angle_refined_deg1.553
r_mcangle_it1.292
r_mcbond_it1.068
r_angle_other_deg0.931
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.227
r_dihedral_angle_4_deg21.704
r_dihedral_angle_3_deg13.392
r_dihedral_angle_1_deg6.819
r_scangle_it2.944
r_scbond_it2.241
r_angle_refined_deg1.553
r_mcangle_it1.292
r_mcbond_it1.068
r_angle_other_deg0.931
r_symmetry_vdw_refined0.326
r_symmetry_vdw_other0.278
r_mcbond_other0.233
r_nbd_other0.209
r_symmetry_hbond_refined0.203
r_nbd_refined0.188
r_nbtor_refined0.172
r_xyhbond_nbd_refined0.141
r_chiral_restr0.097
r_nbtor_other0.085
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3443
Nucleic Acid Atoms
Solvent Atoms466
Heterogen Atoms

Software

Software
Software NamePurpose
d*TREKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling