3UDH

Crystal Structure of BACE with Compound 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION298protein in sodium borate, pH 8.5, reservoir: 30% PEG200, 0.1 M sodium acetate, pH 5.2-5.4, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1442.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.803α = 90
b = 103.75β = 90
c = 99.593γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2008-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-BM1.0APS17-BM

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
11.746.0398.70.04313.14.7341969
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)
11.71.7790.50.4172.83.81

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONRIGID BODY REFINEMENTTHROUGHOUT1.746.0339787213898.550.198260.195940.24137RANDOM24.283
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]
-0.13-0.190.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.102
r_dihedral_angle_4_deg16.758
r_dihedral_angle_3_deg14.195
r_dihedral_angle_1_deg7.779
r_scangle_it5.606
r_scbond_it3.519
r_mcangle_it2.535
r_mcbond_it1.501
r_angle_refined_deg1.216
r_angle_other_deg0.758
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.102
r_dihedral_angle_4_deg16.758
r_dihedral_angle_3_deg14.195
r_dihedral_angle_1_deg7.779
r_scangle_it5.606
r_scbond_it3.519
r_mcangle_it2.535
r_mcbond_it1.501
r_angle_refined_deg1.216
r_angle_other_deg0.758
r_mcbond_other0.46
r_xyhbond_nbd_refined0.299
r_symmetry_vdw_other0.242
r_symmetry_vdw_refined0.238
r_symmetry_hbond_refined0.201
r_chiral_restr0.085
r_xyhbond_nbd_other0.019
r_gen_planes_refined0.012
r_bond_refined_d0.011
r_gen_planes_other0.001
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3106
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms39

Software

Software
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
autoBUSTERphasing