3UFL

Discovery of Pyrrolidine-based b-Secretase Inhibitors: Lead Advancement through Conformational Design for Maintenance of Ligand Binding Efficiency


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7273pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.9958.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.668α = 90
b = 127.642β = 90
c = 76.846γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

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
11.95098.90.07210.16.6403273987011
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)
11.91.97920.4574.53675

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.931.914032739826203898.720.21390.21390.21220.2454RANDOM29.8936
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]
-0.230.44-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.672
r_dihedral_angle_4_deg16.676
r_dihedral_angle_3_deg12.86
r_dihedral_angle_1_deg6.28
r_scangle_it1.979
r_angle_refined_deg1.158
r_scbond_it1.158
r_mcangle_it1.097
r_mcbond_it0.617
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.672
r_dihedral_angle_4_deg16.676
r_dihedral_angle_3_deg12.86
r_dihedral_angle_1_deg6.28
r_scangle_it1.979
r_angle_refined_deg1.158
r_scbond_it1.158
r_mcangle_it1.097
r_mcbond_it0.617
r_nbtor_refined0.31
r_symmetry_vdw_refined0.237
r_nbd_refined0.186
r_symmetry_hbond_refined0.152
r_xyhbond_nbd_refined0.123
r_chiral_restr0.089
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2927
Nucleic Acid Atoms
Solvent Atoms308
Heterogen Atoms66

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOLREPphasing