7DJI

Crystal structure of Lymnaea stagnalis Acetylcholine binding protein (AChBP) complexed with Paraherquamide A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZJU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP529814.1-15.6% PEG 4000, Sodium Citrate buffer pH 5.0
Crystal Properties
Matthews coefficientSolvent content
2.448.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.373α = 90
b = 74.373β = 90
c = 349.595γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2017-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.0SPring-8BL26B1

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
12.247.3741000.07121.710.855263
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)
12.22.261000.7137.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2ZJU2.247.3755135273499.90.1850.23149.02
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]
0.5650.2820.565-1.832
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.391
r_dihedral_angle_4_deg16.604
r_dihedral_angle_3_deg14.299
r_dihedral_angle_1_deg7.481
r_mcangle_it1.571
r_mcangle_other1.571
r_angle_refined_deg1.413
r_scangle_it1.254
r_scangle_other1.254
r_angle_other_deg1.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.391
r_dihedral_angle_4_deg16.604
r_dihedral_angle_3_deg14.299
r_dihedral_angle_1_deg7.481
r_mcangle_it1.571
r_mcangle_other1.571
r_angle_refined_deg1.413
r_scangle_it1.254
r_scangle_other1.254
r_angle_other_deg1.15
r_mcbond_it0.872
r_mcbond_other0.872
r_scbond_it0.707
r_scbond_other0.707
r_nbd_refined0.169
r_nbd_other0.159
r_nbtor_refined0.158
r_xyhbond_nbd_refined0.128
r_chiral_restr0.048
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbtor_other
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_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 Atoms8176
Nucleic Acid Atoms
Solvent Atoms486
Heterogen Atoms250

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building