2ZJH

Crystal structure of the human BACE1 catalytic domain in complex with N-(1-benzyl-piperidin-4-yl)-4-mercapto-butyramide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52950.1M Bis-Tris pH 6.5, 0.1M sodium chloride, 1.5M ammonium sulfate, 7.0 mg/ml Beta-secretase 1 , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.8957.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.596α = 90
b = 103.596β = 90
c = 168.741γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray180IMAGE PLATERIGAKU RAXIS IV2004-02-10MSINGLE 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
12.620990.11110.81711816879
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)
12.62.690.432

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 2P8H2.6201584884497.840.228930.226840.26859RANDOM38.902
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]
-0.38-0.19-0.380.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.136
r_dihedral_angle_4_deg17.615
r_dihedral_angle_3_deg15.351
r_dihedral_angle_1_deg5.705
r_mcangle_it3.196
r_scangle_it2.352
r_mcbond_it1.896
r_scbond_it1.519
r_angle_refined_deg0.964
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.136
r_dihedral_angle_4_deg17.615
r_dihedral_angle_3_deg15.351
r_dihedral_angle_1_deg5.705
r_mcangle_it3.196
r_scangle_it2.352
r_mcbond_it1.896
r_scbond_it1.519
r_angle_refined_deg0.964
r_nbtor_refined0.305
r_nbd_refined0.178
r_symmetry_vdw_refined0.157
r_xyhbond_nbd_refined0.125
r_symmetry_hbond_refined0.064
r_chiral_restr0.061
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 Atoms2771
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms20

Software

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