3WZP

Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with iminobiotin long tail (IMNtail) at 1.2 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.2 M sodium citrate tribasic dehydrate, 0.1 M HEPES sodium, 35%(w/v) (+/-)-2-methyl-2, 4-pentandiol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2845.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.969α = 90
b = 57.5β = 103.34
c = 71.807γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2012-10-16MSINGLE 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
11.25096.60.06818.33.5148314143314
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)
11.21.2496.60.3092.753.5148314

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 REPLACEMENTTHROUGHOUT3WYQ1.215135778718496.490.134870.13350.16056RANDOM11.669
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]
0.070.1-0.150.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.15
r_dihedral_angle_3_deg11.262
r_dihedral_angle_4_deg10.244
r_dihedral_angle_1_deg7.12
r_scangle_it6.592
r_scbond_it5.039
r_mcangle_it4.224
r_mcbond_it2.97
r_rigid_bond_restr2.749
r_angle_refined_deg2.272
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.15
r_dihedral_angle_3_deg11.262
r_dihedral_angle_4_deg10.244
r_dihedral_angle_1_deg7.12
r_scangle_it6.592
r_scbond_it5.039
r_mcangle_it4.224
r_mcbond_it2.97
r_rigid_bond_restr2.749
r_angle_refined_deg2.272
r_chiral_restr0.323
r_bond_refined_d0.026
r_gen_planes_refined0.015
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 Atoms3594
Nucleic Acid Atoms
Solvent Atoms441
Heterogen Atoms126

Software

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