3DM6

Beta-secretase 1 complexed with statine-based inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529916% PEG8000, 0.1M Citrate, 0.3M Lithium sulphate, 0.1M Sodium Chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 299K
Crystal Properties
Matthews coefficientSolvent content
3.1661.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.435α = 90
b = 103.017β = 103.5
c = 103.11γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2006-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9340ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.6100.50497.80.0540.0549.63.9510521.51.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.62.7497.70.4160.4161.83.97378

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUT2.663.761.55229048421260597.580.2530.225860.22290.28131RANDOM65.052
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]
0.06-0.04-0.07-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.604
r_dihedral_angle_3_deg19.248
r_dihedral_angle_4_deg18.935
r_dihedral_angle_1_deg6.967
r_scangle_it2.278
r_angle_refined_deg1.501
r_scbond_it1.411
r_mcangle_it1.358
r_mcbond_it0.763
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.604
r_dihedral_angle_3_deg19.248
r_dihedral_angle_4_deg18.935
r_dihedral_angle_1_deg6.967
r_scangle_it2.278
r_angle_refined_deg1.501
r_scbond_it1.411
r_mcangle_it1.358
r_mcbond_it0.763
r_nbtor_refined0.319
r_symmetry_vdw_refined0.236
r_nbd_refined0.223
r_symmetry_hbond_refined0.169
r_xyhbond_nbd_refined0.157
r_chiral_restr0.101
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8704
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms186

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction