2OHM

X-ray crystal structure of beta secretase complexed with N~3~-benzylpyridine-2,3-diamine


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
2.8156.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.172α = 90
b = 101.172β = 90
c = 170.924γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.20.97800SRSPX14.2

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
12.742.4496.60.1391433514335

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 1W502.742.44143351433572996.590.2140.2140.2110.279RANDOM37.579
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]
-0.98-0.49-0.981.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.681
r_dihedral_angle_3_deg17.715
r_dihedral_angle_4_deg15.095
r_dihedral_angle_1_deg7.224
r_angle_refined_deg1.43
r_angle_other_deg0.868
r_nbd_refined0.213
r_symmetry_vdw_other0.211
r_nbd_other0.204
r_nbtor_refined0.193
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.681
r_dihedral_angle_3_deg17.715
r_dihedral_angle_4_deg15.095
r_dihedral_angle_1_deg7.224
r_angle_refined_deg1.43
r_angle_other_deg0.868
r_nbd_refined0.213
r_symmetry_vdw_other0.211
r_nbd_other0.204
r_nbtor_refined0.193
r_symmetry_vdw_refined0.188
r_symmetry_hbond_refined0.161
r_xyhbond_nbd_refined0.126
r_nbtor_other0.09
r_scangle_it0.09
r_chiral_restr0.076
r_mcangle_it0.074
r_scbond_it0.069
r_mcbond_it0.047
r_mcbond_other0.014
r_bond_refined_d0.012
r_xyhbond_nbd_other0.012
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 Atoms2966
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms21

Software

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