3DXC

Crystal structure of the intracellular domain of human APP in complex with Fe65-PTB2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.62933.2 M NaCl,0.1 M sodium acetate , pH 4.6, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6165.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.32α = 90
b = 114.32β = 90
c = 74.85γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42007-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-21.00ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.1331000.060.0628.811.132612
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.210.4650.4654.711.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.1333057919971000.204490.202290.23816RANDOM41.32
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]
-0.07-0.03-0.070.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.832
r_dihedral_angle_4_deg14.396
r_dihedral_angle_3_deg14.21
r_dihedral_angle_1_deg6.377
r_scangle_it3.23
r_scbond_it2.188
r_mcangle_it1.71
r_angle_refined_deg1.312
r_mcbond_it1.003
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.832
r_dihedral_angle_4_deg14.396
r_dihedral_angle_3_deg14.21
r_dihedral_angle_1_deg6.377
r_scangle_it3.23
r_scbond_it2.188
r_mcangle_it1.71
r_angle_refined_deg1.312
r_mcbond_it1.003
r_nbtor_refined0.297
r_symmetry_vdw_refined0.219
r_nbd_refined0.206
r_symmetry_hbond_refined0.191
r_xyhbond_nbd_refined0.182
r_chiral_restr0.089
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms2395
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing