5NAP

Torpedo californica acetylcholinesterase in complex with a non-chiral donepezil-like inhibitor 17


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5E4T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277.15MES 100 mM, pH 6.2 PEG 200 30%
Crystal Properties
Matthews coefficientSolvent content
4.0169.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.53α = 90
b = 111.53β = 90
c = 136.88γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2016-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.0ELETTRA5.2R

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
12.1778.921000.1199.25.952442
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)
12.172.291000.5263.15.8

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 REPLACEMENTTHROUGHOUT5E4T2.1755.949664270599.90.1720.170.21RANDOM30.66
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]
0.850.850.85-2.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.003
r_dihedral_angle_4_deg16.832
r_dihedral_angle_3_deg14.57
r_long_range_B_refined7.239
r_long_range_B_other7.175
r_dihedral_angle_1_deg6.762
r_scangle_other6.187
r_scbond_it4.24
r_scbond_other4.239
r_mcangle_other3.625
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.003
r_dihedral_angle_4_deg16.832
r_dihedral_angle_3_deg14.57
r_long_range_B_refined7.239
r_long_range_B_other7.175
r_dihedral_angle_1_deg6.762
r_scangle_other6.187
r_scbond_it4.24
r_scbond_other4.239
r_mcangle_other3.625
r_mcangle_it3.621
r_mcbond_it2.626
r_mcbond_other2.616
r_angle_refined_deg2.037
r_angle_other_deg0.995
r_chiral_restr0.127
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4206
Nucleic Acid Atoms
Solvent Atoms425
Heterogen Atoms152

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing