3UDK

Crystal Structure of BACE with Compound 6


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
2.1943.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.797α = 90
b = 104.425β = 90
c = 101.333γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTC2008-09-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.5418

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
12.55099.60.0817.94.813884
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)
12.52.5999.60.5814.4

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 REFINEMENTTHROUGHOUT2.5130.141314771799.380.223070.218620.30562RANDOM30.466
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]
-0.14-0.280.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.971
r_dihedral_angle_3_deg16.807
r_dihedral_angle_4_deg15.673
r_dihedral_angle_1_deg8.805
r_scangle_it3.418
r_scbond_it2.171
r_mcangle_it1.588
r_mcbond_it0.871
r_angle_refined_deg0.869
r_angle_other_deg0.607
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.971
r_dihedral_angle_3_deg16.807
r_dihedral_angle_4_deg15.673
r_dihedral_angle_1_deg8.805
r_scangle_it3.418
r_scbond_it2.171
r_mcangle_it1.588
r_mcbond_it0.871
r_angle_refined_deg0.869
r_angle_other_deg0.607
r_mcbond_other0.165
r_chiral_restr0.059
r_gen_planes_refined0.009
r_bond_refined_d0.007
r_gen_planes_other0.001
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms3102
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms40

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction