2OHS

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


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
2.8156.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.303α = 90
b = 101.303β = 90
c = 170.355γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2004-02-23MSINGLE 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
12.4550.6595.80.1181868118681

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1W502.4550.65186811868194794.890.1850.1850.1820.251RANDOM24.868
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]
-0.93-0.46-0.931.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.052
r_dihedral_angle_4_deg17.123
r_dihedral_angle_3_deg16.474
r_dihedral_angle_1_deg6.872
r_angle_refined_deg1.478
r_angle_other_deg0.988
r_symmetry_vdw_other0.254
r_nbd_refined0.208
r_nbd_other0.205
r_symmetry_vdw_refined0.197
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.052
r_dihedral_angle_4_deg17.123
r_dihedral_angle_3_deg16.474
r_dihedral_angle_1_deg6.872
r_angle_refined_deg1.478
r_angle_other_deg0.988
r_symmetry_vdw_other0.254
r_nbd_refined0.208
r_nbd_other0.205
r_symmetry_vdw_refined0.197
r_nbtor_refined0.191
r_xyhbond_nbd_refined0.185
r_chiral_restr0.154
r_scangle_it0.127
r_symmetry_hbond_refined0.118
r_scbond_it0.1
r_mcangle_it0.091
r_nbtor_other0.089
r_mcbond_it0.062
r_mcbond_other0.022
r_bond_refined_d0.013
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2948
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms48

Software

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