5YEE

Crystal structure of LokiProfilin1/Rabbit Actin Complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HBT3HBT, 5YED
experimental modelPDB 5YED3HBT, 5YED

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7291100 mM Hepes, pH 7.0, 20 % w/v Polyethylene glycol 6,000, 200 mM NaCl, 10 mM ATP disodium salt
Crystal Properties
Matthews coefficientSolvent content
2.5651.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.312α = 90
b = 126.209β = 97.89
c = 53.862γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2017-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.8163.199.511.95.449614
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.8478.50.6923.4

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 REPLACEMENTTHROUGHOUT3HBT, 5YED1.8163.149614256199.470.194220.191350.24864RANDOM30.492
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]
0.06-0.01-0.05-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.505
r_dihedral_angle_4_deg15.09
r_dihedral_angle_3_deg15.055
r_dihedral_angle_1_deg6.699
r_long_range_B_refined6.673
r_long_range_B_other6.551
r_scangle_other4.808
r_mcangle_it3.42
r_mcangle_other3.419
r_scbond_it3.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.505
r_dihedral_angle_4_deg15.09
r_dihedral_angle_3_deg15.055
r_dihedral_angle_1_deg6.699
r_long_range_B_refined6.673
r_long_range_B_other6.551
r_scangle_other4.808
r_mcangle_it3.42
r_mcangle_other3.419
r_scbond_it3.28
r_scbond_other3.28
r_mcbond_it2.519
r_mcbond_other2.519
r_angle_refined_deg1.943
r_angle_other_deg1.093
r_chiral_restr0.119
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.003
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 Atoms3837
Nucleic Acid Atoms
Solvent Atoms596
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing