3WZO

Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with biotin long tail (BTNtail) at 1.5 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62930.1 M cadmium chloride hydrate, 0.1 M sodium acetate trihydrate, 30%(v/v) PEG400, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9235.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.241α = 90
b = 85.461β = 90
c = 86.115γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98000Photon FactoryBL-17A

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
11.55097.40.03517.66.36572464012
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)
11.51.5597.40.2323.086.364012

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 REPLACEMENTTHROUGHOUT3WYQ1.55060475323596.940.176130.17290.23616RANDOM15.935
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]
-0.41.66-1.26
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free40.256
r_dihedral_angle_2_deg26.406
r_dihedral_angle_3_deg14.443
r_dihedral_angle_4_deg12.47
r_sphericity_bonded10.738
r_dihedral_angle_1_deg7.272
r_scangle_other5.436
r_long_range_B_other5.177
r_long_range_B_refined5.176
r_scbond_other4.779
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free40.256
r_dihedral_angle_2_deg26.406
r_dihedral_angle_3_deg14.443
r_dihedral_angle_4_deg12.47
r_sphericity_bonded10.738
r_dihedral_angle_1_deg7.272
r_scangle_other5.436
r_long_range_B_other5.177
r_long_range_B_refined5.176
r_scbond_other4.779
r_scbond_it4.778
r_rigid_bond_restr3.63
r_mcangle_other3.619
r_mcangle_it3.618
r_mcbond_it2.999
r_mcbond_other2.952
r_angle_refined_deg1.912
r_angle_other_deg0.877
r_chiral_restr0.135
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms3652
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms159

Software

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