2PH8

Crystal Structure of Human Beta Secretase Complexed with inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293Crystals were grown with L124671 and inhibitor was back soaked in the crystal at pH 5.0. 1.5M LITHIUM SULFATE, 0.1M HEPES BUFFER, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8256.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.811α = 90
b = 128.523β = 90
c = 76.276γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2007-03-15MSINGLE 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
11.7301000.04636.36.256340
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)
1.71.761000.493.45.9

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 1TQF1.73053441285799.920.185960.185010.20387RANDOM27.379
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]
-1.112.27-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.11
r_dihedral_angle_4_deg21.277
r_dihedral_angle_3_deg12.232
r_dihedral_angle_1_deg5.962
r_scangle_it3.111
r_scbond_it1.939
r_mcangle_it1.352
r_angle_refined_deg1.215
r_mcbond_it0.851
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.11
r_dihedral_angle_4_deg21.277
r_dihedral_angle_3_deg12.232
r_dihedral_angle_1_deg5.962
r_scangle_it3.111
r_scbond_it1.939
r_mcangle_it1.352
r_angle_refined_deg1.215
r_mcbond_it0.851
r_nbtor_refined0.313
r_nbd_refined0.191
r_symmetry_vdw_refined0.19
r_symmetry_hbond_refined0.137
r_xyhbond_nbd_refined0.12
r_chiral_restr0.084
r_bond_refined_d0.009
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 Atoms2871
Nucleic Acid Atoms
Solvent Atoms293
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing