5MCQ

CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH ACTIVE SITE AND EXOSITE BINDING PEPTIDE INHIBITOR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherunpublished structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52950.1M magnesium acetate, 0.1M sodium acetate, 8% (w/v) PEG8000
Crystal Properties
Matthews coefficientSolvent content
3.6566.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.93α = 90
b = 101.93β = 90
c = 116.35γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.8248.5899.90.081316.710.2463008
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.9199.91.310.13

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 REPLACEMENTTHROUGHOUTunpublished structure1.8248.5859801316999.940.180070.177740.22424RANDOM33.565
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]
0.510.250.51-1.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.19
r_dihedral_angle_4_deg17.696
r_dihedral_angle_3_deg14.25
r_long_range_B_refined9.087
r_dihedral_angle_1_deg6.99
r_mcangle_it4.347
r_scbond_it4.197
r_mcbond_it2.922
r_angle_refined_deg1.932
r_chiral_restr0.134
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.19
r_dihedral_angle_4_deg17.696
r_dihedral_angle_3_deg14.25
r_long_range_B_refined9.087
r_dihedral_angle_1_deg6.99
r_mcangle_it4.347
r_scbond_it4.197
r_mcbond_it2.922
r_angle_refined_deg1.932
r_chiral_restr0.134
r_bond_refined_d0.02
r_gen_planes_refined0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3248
Nucleic Acid Atoms
Solvent Atoms586
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing