2OHR

X-ray crystal structure of beta secretase complexed with compound 6a


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
2.8356.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.03α = 90
b = 101.03β = 90
c = 172.33γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2003-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-30.93100ESRFID14-3

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
12.2550.5298.70.1052490324903

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 1W502.2550.520.1732490324903127198.110.1730.170.214RANDOM25.206
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]
-1.32-0.66-1.321.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.715
r_dihedral_angle_4_deg16.602
r_dihedral_angle_3_deg14.924
r_dihedral_angle_1_deg7.085
r_angle_refined_deg1.424
r_angle_other_deg0.876
r_symmetry_vdw_other0.238
r_xyhbond_nbd_refined0.229
r_symmetry_hbond_refined0.229
r_nbd_other0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.715
r_dihedral_angle_4_deg16.602
r_dihedral_angle_3_deg14.924
r_dihedral_angle_1_deg7.085
r_angle_refined_deg1.424
r_angle_other_deg0.876
r_symmetry_vdw_other0.238
r_xyhbond_nbd_refined0.229
r_symmetry_hbond_refined0.229
r_nbd_other0.21
r_nbd_refined0.201
r_nbtor_refined0.186
r_symmetry_vdw_refined0.172
r_scangle_it0.11
r_mcangle_it0.093
r_scbond_it0.091
r_nbtor_other0.09
r_chiral_restr0.085
r_mcbond_it0.07
r_mcbond_other0.031
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 Atoms279
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ProDCdata collection
MOSFLMdata reduction
CCP4data scaling
C-SEARCHphasing