8XSU | pdb_00008xsu

Crystal Structure of Lymnaea stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Dinotefuran


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.4293PEG4000 16.5 - 18.0% , sodium citrate 0.2M
Crystal Properties
Matthews coefficientSolvent content
2.3647.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.149α = 90
b = 74.149β = 90
c = 350.306γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2017-06-19MSINGLE 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)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
12.6347.3499.90.0940.1030.0430.9992211.332196
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)
12.632.7699.70.8270.910.3790.94911.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.63247.3432089162999.8880.1980.19550.19760.25380.25473.292
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]
1.9970.9981.997-6.477
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.771
r_dihedral_angle_6_deg13.395
r_lrange_it8.904
r_lrange_other8.904
r_dihedral_angle_2_deg8.556
r_dihedral_angle_1_deg7.455
r_scangle_it5.647
r_scangle_other5.646
r_mcangle_it5.235
r_mcangle_other5.235
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8285
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms140

Software

Software
Software NamePurpose
XDSdata scaling
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement