2VA5

X-ray crystal structure of beta secretase complexed with compound 8c


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120-22.5% (W/V) PEG 5000 MONOMETHYLETHYL (MME), 200 MM SODIUM CITRATE (PH 6.6) AND 200 MM AMMONIUM IODIDE
Crystal Properties
Matthews coefficientSolvent content
2.9658.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.138α = 90
b = 102.138β = 90
c = 168.258γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.1SRSPX14.1

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
12.755098.80.122.413125
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.752.8299.90.46

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 1W502.7551.071312569097.90.2320.2280.319RANDOM38.27
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]
0.360.180.36-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.384
r_dihedral_angle_3_deg17.135
r_dihedral_angle_4_deg16.251
r_dihedral_angle_1_deg7.472
r_angle_refined_deg1.391
r_angle_other_deg0.872
r_symmetry_vdw_refined0.219
r_nbd_refined0.214
r_nbd_other0.202
r_symmetry_vdw_other0.193
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.384
r_dihedral_angle_3_deg17.135
r_dihedral_angle_4_deg16.251
r_dihedral_angle_1_deg7.472
r_angle_refined_deg1.391
r_angle_other_deg0.872
r_symmetry_vdw_refined0.219
r_nbd_refined0.214
r_nbd_other0.202
r_symmetry_vdw_other0.193
r_nbtor_refined0.192
r_symmetry_hbond_refined0.192
r_xyhbond_nbd_refined0.188
r_nbtor_other0.089
r_scangle_it0.087
r_chiral_restr0.078
r_mcangle_it0.074
r_scbond_it0.069
r_mcbond_it0.047
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2966
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
C-SEARCHphasing