2OF0

X-ray crystal structure of beta secretase complexed with compound 5


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.629320-22.5% (w/v) PEG 5000 monomethylether (MME), 200 mM sodium citrate (pH 6.6), 200 mM ammonium iodide, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9758.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.412α = 90
b = 102.412β = 90
c = 169.237γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2002-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54180

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
12.238.22690524904

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 REPLACEMENTTHROUGHOUTPDB entry 1W502.2538.1923631127897.330.2230.220.28RANDOM36.407
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]
-0.37-0.19-0.370.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.126
r_dihedral_angle_3_deg14.774
r_dihedral_angle_4_deg12.739
r_dihedral_angle_1_deg6.986
r_angle_refined_deg1.407
r_angle_other_deg0.89
r_symmetry_vdw_other0.251
r_nbd_other0.204
r_nbd_refined0.193
r_symmetry_vdw_refined0.188
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.126
r_dihedral_angle_3_deg14.774
r_dihedral_angle_4_deg12.739
r_dihedral_angle_1_deg6.986
r_angle_refined_deg1.407
r_angle_other_deg0.89
r_symmetry_vdw_other0.251
r_nbd_other0.204
r_nbd_refined0.193
r_symmetry_vdw_refined0.188
r_nbtor_refined0.185
r_xyhbond_nbd_refined0.147
r_symmetry_hbond_refined0.113
r_nbtor_other0.089
r_scangle_it0.089
r_chiral_restr0.079
r_mcangle_it0.076
r_scbond_it0.073
r_mcbond_it0.055
r_mcbond_other0.021
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2966
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction
CCP4data scaling
CSearchphasing