3WYP

Crystal structure of wild-type core streptavidin in complex with D-biotin/biotin-D-sulfoxide at 1.3 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2F01 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.22930.2M ammonium sulfate, 0.1M sodium acetate trihydrate, 24% polyethylene glycol 4000, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.354α = 90
b = 97.696β = 112.29
c = 52.57γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2011-11-15MSINGLE 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
11.350960.04623.4113295110519
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)
11.31.3293.30.3452.91

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 REPLACEMENTTHROUGHOUT2F011.326.69104885553895.680.133020.130610.17875RANDOM11.664
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]
-0.09-0.080.12-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.516
r_dihedral_angle_4_deg23.126
r_dihedral_angle_3_deg12.279
r_dihedral_angle_1_deg7.602
r_scangle_it6.191
r_scbond_it4.735
r_mcangle_it3.668
r_rigid_bond_restr2.681
r_mcbond_it2.642
r_angle_refined_deg2.232
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.516
r_dihedral_angle_4_deg23.126
r_dihedral_angle_3_deg12.279
r_dihedral_angle_1_deg7.602
r_scangle_it6.191
r_scbond_it4.735
r_mcangle_it3.668
r_rigid_bond_restr2.681
r_mcbond_it2.642
r_angle_refined_deg2.232
r_chiral_restr0.166
r_bond_refined_d0.025
r_gen_planes_refined0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3630
Nucleic Acid Atoms
Solvent Atoms480
Heterogen Atoms136

Software

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