5O8T

Crystal structure of wild type Aplysia californica AChBP in complex with strychnine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293Reservoir contained 0.1 M magnesium chloride, 25% PEG 3350. Protein buffer 50 mm tris, 250 mM NaCl, pH 7.5. 0.5 mM strychnine
Crystal Properties
Matthews coefficientSolvent content
2.3948.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.46α = 90
b = 74.46β = 90
c = 186.754γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray150PIXELDECTRIS PILATUS 6M-F2015-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.91739DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.228.6399.10.1350.9948.55.55831823.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2499.70.7620.5522.35.7

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 REPLACEMENTTHROUGHOUT2xys2.228.6355431282899.050.183470.181160.22855RANDOM35.142
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]
-0.03-0.01-0.030.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.335
r_dihedral_angle_4_deg17.688
r_dihedral_angle_3_deg13.519
r_long_range_B_other13.505
r_long_range_B_refined13.472
r_scangle_other12.267
r_scbond_it9.536
r_scbond_other9.532
r_mcangle_it8.533
r_mcangle_other8.533
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.335
r_dihedral_angle_4_deg17.688
r_dihedral_angle_3_deg13.519
r_long_range_B_other13.505
r_long_range_B_refined13.472
r_scangle_other12.267
r_scbond_it9.536
r_scbond_other9.532
r_mcangle_it8.533
r_mcangle_other8.533
r_mcbond_it6.651
r_mcbond_other6.646
r_dihedral_angle_1_deg6.409
r_angle_refined_deg1.378
r_angle_other_deg0.908
r_chiral_restr0.079
r_bond_refined_d0.009
r_bond_other_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
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 Atoms8202
Nucleic Acid Atoms
Solvent Atoms588
Heterogen Atoms195

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing