6QQP

Aplysia californica AChBP in complex with 2-Fluoro-(carbamoylpyridinyl)deschloroepibatidine analogue (2)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5O87 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.2293Reservoir: 0.2 M NaCl, 0.1 M Phosphate/citrate pH 4.2 8% PEG 8000 Buffer: 50 mM Tris 250 mM NaCl pH 7.5 Protein concentration: 4 mg/ml Microseeded
Crystal Properties
Matthews coefficientSolvent content
3.4964.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 209.53α = 90
b = 136.948β = 102.74
c = 131.552γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.968580DiamondI24

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
12.446.8298.70.0890.958.22.913919929
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)
12.42.4498.70.510.652.52.8

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 REPLACEMENTTHROUGHOUT5o872.446.82131926690398.250.188930.187850.21003RANDOM34.364
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]
-2.47-0.223.82-1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.612
r_dihedral_angle_4_deg16.194
r_dihedral_angle_3_deg13.479
r_dihedral_angle_1_deg8.064
r_long_range_B_refined7.437
r_long_range_B_other7.397
r_scangle_other5.388
r_mcangle_it3.638
r_mcangle_other3.638
r_scbond_it3.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.612
r_dihedral_angle_4_deg16.194
r_dihedral_angle_3_deg13.479
r_dihedral_angle_1_deg8.064
r_long_range_B_refined7.437
r_long_range_B_other7.397
r_scangle_other5.388
r_mcangle_it3.638
r_mcangle_other3.638
r_scbond_it3.307
r_scbond_other3.307
r_mcbond_it2.264
r_mcbond_other2.264
r_angle_refined_deg1.49
r_angle_other_deg0.919
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms16388
Nucleic Acid Atoms
Solvent Atoms924
Heterogen Atoms610

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing