2QZL

Crystal Structure of human Beta Secretase complexed with IXS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TQFPDB entry 1TQF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52931.5M LITHIUM SULFATE, 0.1M HEPES BUFFER, Crystals were grown with inhibitors were back soaked, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.856.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.931α = 90
b = 128.152β = 90
c = 76.307γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

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

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
11.85099.30.05328.54.547976
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.86990.525.34

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB entry 1TQF1.82040677216989.330.217460.216210.24107RANDOM19.496
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]
-0.752.06-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.794
r_dihedral_angle_4_deg22.947
r_dihedral_angle_3_deg14.412
r_dihedral_angle_1_deg5.984
r_scangle_it2.2
r_scbond_it1.374
r_angle_refined_deg1.176
r_mcangle_it0.961
r_mcbond_it0.581
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.794
r_dihedral_angle_4_deg22.947
r_dihedral_angle_3_deg14.412
r_dihedral_angle_1_deg5.984
r_scangle_it2.2
r_scbond_it1.374
r_angle_refined_deg1.176
r_mcangle_it0.961
r_mcbond_it0.581
r_nbtor_refined0.31
r_nbd_refined0.193
r_symmetry_hbond_refined0.193
r_symmetry_vdw_refined0.17
r_xyhbond_nbd_refined0.119
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms2961
Nucleic Acid Atoms
Solvent Atoms411
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
REFMACphasing