3X00

Crystal structure of the core streptavidin mutant V212 (Y22S/N23D/S27D/S45N/Y83S/R84K/E101D/R103K/E116N) complexed with bis iminobiotin long tail (Bis-IMNtail) at 1.3 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WYQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.42930.2 M sodium fluoride, 20% PEG3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1342.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.354α = 90
b = 77.377β = 90
c = 174.122γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2013-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90000SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.35099.60.05635.88127717127145
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3599.60.3583.868127717

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 REPLACEMENTTHROUGHOUT3WYQ1.350120725638499.540.147780.145650.18787RANDOM22.869
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]
0.910.54-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.41
r_dihedral_angle_4_deg27.757
r_sphericity_free26.955
r_dihedral_angle_3_deg13.838
r_sphericity_bonded13.462
r_dihedral_angle_1_deg6.888
r_long_range_B_refined6.048
r_long_range_B_other5.993
r_mcangle_other5.746
r_mcangle_it5.726
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.41
r_dihedral_angle_4_deg27.757
r_sphericity_free26.955
r_dihedral_angle_3_deg13.838
r_sphericity_bonded13.462
r_dihedral_angle_1_deg6.888
r_long_range_B_refined6.048
r_long_range_B_other5.993
r_mcangle_other5.746
r_mcangle_it5.726
r_scangle_other5.524
r_rigid_bond_restr5.425
r_mcbond_it4.715
r_scbond_it4.687
r_scbond_other4.685
r_mcbond_other4.659
r_angle_refined_deg2.23
r_angle_other_deg1.05
r_chiral_restr0.379
r_bond_refined_d0.022
r_gen_planes_refined0.01
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3624
Nucleic Acid Atoms
Solvent Atoms442
Heterogen Atoms100

Software

Software
Software NamePurpose
BSSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling