2ZJJ

Crystal structure of the human BACE1 catalytic domain in complex with 4-(4-fluoro-benzyl)-piperazine-2-carboxylic acid (2-mercapto-ethyl)-amide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82950.1M imidazole pH 8.0, 0.2M Ca(OAC)2, 10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4549.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.21α = 90
b = 93.289β = 90
c = 100.329γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray180CCDADSC QUANTUM 2102004-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.98ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.22018114

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 2P8H2.2201575087771.770.2310.228890.26859RANDOM34.255
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]
-3.480.473.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.689
r_dihedral_angle_4_deg14.859
r_dihedral_angle_3_deg13.418
r_dihedral_angle_1_deg4.801
r_mcangle_it1.75
r_scangle_it1.312
r_mcbond_it1.029
r_angle_refined_deg0.873
r_scbond_it0.815
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.689
r_dihedral_angle_4_deg14.859
r_dihedral_angle_3_deg13.418
r_dihedral_angle_1_deg4.801
r_mcangle_it1.75
r_scangle_it1.312
r_mcbond_it1.029
r_angle_refined_deg0.873
r_scbond_it0.815
r_nbtor_refined0.301
r_nbd_refined0.15
r_symmetry_hbond_refined0.13
r_symmetry_vdw_refined0.102
r_xyhbond_nbd_refined0.081
r_chiral_restr0.056
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 Atoms2903
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms20

Software

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