3MSL

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
16.627320% PEG 5000MME 180mM Ammonium Iodide and 180mM Sodium Citrate pH6.6 , VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.7655.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.19α = 90
b = 100.19β = 90
c = 172.84γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.461.286.30.1020.10612.911.8917067240.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4689.50.2870.1314.311.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1W502.450.12179381706787086.40.2280.2280.235RANDOM24.11
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]
-0.72-0.36-0.721.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.79
r_dihedral_angle_4_deg14.17
r_dihedral_angle_3_deg13.727
r_dihedral_angle_1_deg5.434
r_angle_refined_deg1.036
r_mcangle_it0.59
r_scangle_it0.332
r_mcbond_it0.328
r_scbond_it0.184
r_chiral_restr0.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.79
r_dihedral_angle_4_deg14.17
r_dihedral_angle_3_deg13.727
r_dihedral_angle_1_deg5.434
r_angle_refined_deg1.036
r_mcangle_it0.59
r_scangle_it0.332
r_mcbond_it0.328
r_scbond_it0.184
r_chiral_restr0.068
r_bond_refined_d0.006
r_gen_planes_refined0.003
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 Atoms2965
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms27

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling