3MSK

Fragment Based Discovery and Optimisation of BACE-1 Inhibitors


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W50PDB ENTRY 1W50

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.629321% PEG 5000 MME 175mM Ammonium Iodide and 200mM Sodium Citrate , pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8556.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.51α = 90
b = 102.51β = 90
c = 170.528γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
1249.0910034671222.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.05100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1W50249.09346713467118251000.2250.2230.264RANDOM22.19
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]
0.020.010.02-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.147
r_dihedral_angle_3_deg17.88
r_dihedral_angle_4_deg14.07
r_dihedral_angle_1_deg7.355
r_scangle_it4.634
r_scbond_it3.117
r_angle_refined_deg1.989
r_mcangle_it1.957
r_mcbond_it1.162
r_chiral_restr0.145
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.147
r_dihedral_angle_3_deg17.88
r_dihedral_angle_4_deg14.07
r_dihedral_angle_1_deg7.355
r_scangle_it4.634
r_scbond_it3.117
r_angle_refined_deg1.989
r_mcangle_it1.957
r_mcbond_it1.162
r_chiral_restr0.145
r_bond_refined_d0.024
r_gen_planes_refined0.01
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2966
Nucleic Acid Atoms
Solvent Atoms260
Heterogen Atoms31

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling