2PGZ

Crystal structure of Cocaine bound to an ACh-Binding Protein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BYN2BYN, Apo Aplysia AChBP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72910.1M Tris-HCL 10% (w/v) PEG 400, 15% (w/v) PEG 1000, 2ul drop, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.550.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.822α = 90
b = 115.589β = 90
c = 130.879γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray296CCDADSC QUANTUM 210MSINGLE WAVELENGTH
21x-ray296CCDADSC QUANTUM 210MSINGLE WAVELENGTH
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.000ALS8.2.1
2SYNCHROTRONAPS BEAMLINE 19-ID1.000APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
1,21.765099.30.0570.0517.76.513008813008822
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,21.761.8293.60.5230.4283.15.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2BYN, Apo Aplysia AChBP1.7650129999128685131499.50.180260.179960.21018RANDOM29.491
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]
1.17-1.04-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.579
r_dihedral_angle_4_deg19.923
r_dihedral_angle_3_deg12.384
r_dihedral_angle_1_deg6.208
r_scangle_it2.776
r_scbond_it1.849
r_angle_refined_deg1.254
r_mcangle_it1.227
r_mcbond_it0.79
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.579
r_dihedral_angle_4_deg19.923
r_dihedral_angle_3_deg12.384
r_dihedral_angle_1_deg6.208
r_scangle_it2.776
r_scbond_it1.849
r_angle_refined_deg1.254
r_mcangle_it1.227
r_mcbond_it0.79
r_nbtor_refined0.308
r_symmetry_hbond_refined0.23
r_nbd_refined0.196
r_symmetry_vdw_refined0.187
r_xyhbond_nbd_refined0.158
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8421
Nucleic Acid Atoms
Solvent Atoms1141
Heterogen Atoms155

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing