6T9R

Aplysia californica AChBP in complex with a cytisine derivative


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6QKK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7295.15Starting protein concentration 12.5 mg/ml + 6 mM ligand BS82. Crystallised as hanging drops, the drop containing 1.5 ul protein, 0.2 ul reservoir (0.8 M NaH2PO4, 0.8 M KH2PO4, 10% glycerol, 0.1 M HEPES pH 7.0) and 0.3 ul microseeds from cytisine bound AChBP crystals (grown as sitting drops in 0.8 M NaH2PO4, 0.8 M KH2PO4, 0.1 M HEPES pH 7.5).
Crystal Properties
Matthews coefficientSolvent content
3.1460.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 209.466α = 90
b = 132.874β = 102.524
c = 131.086γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.72127.9795.50.070.0950.0640.9937.63.535343225.07
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.7566.60.821.1380.7870.4350.62.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6QKK1.72111.6663533651738895.4590.1630.16190.192230.393
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]
-2.078-0.0752.651-0.491
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.528
r_dihedral_angle_4_deg20.452
r_dihedral_angle_1_deg19.702
r_dihedral_angle_3_deg13.707
r_lrange_it8.358
r_lrange_other8.106
r_scangle_it6.038
r_scangle_other6.038
r_scbond_it4.143
r_scbond_other4.143
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.528
r_dihedral_angle_4_deg20.452
r_dihedral_angle_1_deg19.702
r_dihedral_angle_3_deg13.707
r_lrange_it8.358
r_lrange_other8.106
r_scangle_it6.038
r_scangle_other6.038
r_scbond_it4.143
r_scbond_other4.143
r_mcangle_it3.62
r_mcangle_other3.62
r_mcbond_it2.665
r_mcbond_other2.665
r_angle_other_deg2.474
r_angle_refined_deg1.838
r_symmetry_nbd_refined0.227
r_symmetry_nbd_other0.199
r_nbd_other0.189
r_nbd_refined0.188
r_xyhbond_nbd_refined0.176
r_symmetry_xyhbond_nbd_refined0.171
r_nbtor_refined0.164
r_chiral_restr0.095
r_symmetry_nbtor_other0.086
r_metal_ion_refined0.084
r_symmetry_xyhbond_nbd_other0.067
r_bond_other_d0.034
r_gen_planes_other0.016
r_bond_refined_d0.013
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16425
Nucleic Acid Atoms
Solvent Atoms2899
Heterogen Atoms636

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing