2BYQ

Crystal structure of Aplysia californica AChBP in complex with epibatidine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BYNPDB ENTRY 2BYN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.518-22% PEG-3350, 0.1 M TRIS, PH 7.5, 0.2 M SODIUM CITRATE
Crystal Properties
Matthews coefficientSolvent content
2.8155.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 200.925α = 90
b = 200.925β = 90
c = 200.925γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
13.43097.60.198.33.518257

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 2BYN3.4301713292996.80.1840.180.255RANDOM45.41
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.159
r_dihedral_angle_3_deg20.471
r_dihedral_angle_4_deg18.45
r_dihedral_angle_1_deg7.472
r_angle_refined_deg1.524
r_scangle_it1.292
r_scbond_it0.772
r_mcangle_it0.482
r_nbtor_refined0.319
r_mcbond_it0.271
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.159
r_dihedral_angle_3_deg20.471
r_dihedral_angle_4_deg18.45
r_dihedral_angle_1_deg7.472
r_angle_refined_deg1.524
r_scangle_it1.292
r_scbond_it0.772
r_mcangle_it0.482
r_nbtor_refined0.319
r_mcbond_it0.271
r_symmetry_vdw_refined0.256
r_nbd_refined0.22
r_xyhbond_nbd_refined0.161
r_chiral_restr0.104
r_symmetry_hbond_refined0.094
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_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 Atoms8515
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing