2ZJN

Crystal structure of the human BACE1 catalytic domain in complex with N-[1-(5-chloro-2-isopropoxy-3-methoxy-benzyl)-piperidin-4-yl]-2-(2-methyl-4-sulfamoyl-phenoxy)-acetamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2P8HPDB ENTRY 2P8H

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52956mg/ml BACE1, 0.1M HEPES pH 7.5, 1.5M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.8857.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.989α = 90
b = 103.989β = 90
c = 167.081γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray180IMAGE PLATERIGAKU RAXIS IV2005-01-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54

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
12.72099.70.0971530215191
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)
2.72.80.328

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 2P8H2.7201438574899.280.223950.222120.25977RANDOM38.158
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]
-0.75-0.37-0.751.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.89
r_dihedral_angle_3_deg14.345
r_dihedral_angle_4_deg12.543
r_dihedral_angle_1_deg4.807
r_mcangle_it2.152
r_scangle_it1.549
r_mcbond_it1.241
r_scbond_it0.938
r_angle_refined_deg0.881
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.89
r_dihedral_angle_3_deg14.345
r_dihedral_angle_4_deg12.543
r_dihedral_angle_1_deg4.807
r_mcangle_it2.152
r_scangle_it1.549
r_mcbond_it1.241
r_scbond_it0.938
r_angle_refined_deg0.881
r_nbtor_refined0.302
r_nbd_refined0.163
r_symmetry_vdw_refined0.136
r_xyhbond_nbd_refined0.104
r_symmetry_hbond_refined0.104
r_chiral_restr0.055
r_bond_refined_d0.006
r_gen_planes_refined0.002
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 Atoms2878
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing