3C79

Crystal structure of Aplysia californica AChBP in complex with the neonicotinoid imidacloprid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BYNpdb entry 2byn

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529122% isopropanol, 0.2M magnesium chloride, 0.1 M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5451.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.39α = 90
b = 116.286β = 90
c = 132.463γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979APS19-ID

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
12.4847.7297.70.09518.82.1464144410242.7
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)
12.482.5798.10.4545.87210

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 2byn2.4847.7244045235597.630.190840.187630.25047RANDOM39.48
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]
-0.46-1.091.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.336
r_dihedral_angle_4_deg24.276
r_dihedral_angle_3_deg17.631
r_dihedral_angle_1_deg7.579
r_scangle_it5.63
r_scbond_it3.947
r_mcangle_it2.395
r_angle_refined_deg2.273
r_mcbond_it1.53
r_symmetry_hbond_refined0.577
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.336
r_dihedral_angle_4_deg24.276
r_dihedral_angle_3_deg17.631
r_dihedral_angle_1_deg7.579
r_scangle_it5.63
r_scbond_it3.947
r_mcangle_it2.395
r_angle_refined_deg2.273
r_mcbond_it1.53
r_symmetry_hbond_refined0.577
r_nbtor_refined0.329
r_nbd_refined0.233
r_symmetry_vdw_refined0.204
r_chiral_restr0.152
r_xyhbond_nbd_refined0.149
r_bond_refined_d0.028
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8414
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing