3RY2

Wild-type core streptavidin-biotin complex at atomic resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MK5PDB entry 1MK5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.529830% saturated ammonium sulfate, 0.1 M sodium acetate, 0.2 M sodium chloride, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1542.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.426α = 90
b = 94.062β = 90
c = 104.608γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2003-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.9794SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
10.8870.0183.40.04949.14150014150014
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.880.99.4836

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONisomorphous to previous structureTHROUGHOUTPDB entry 1MK50.9550137368137368691495.620.11610.11610.11530.1313RANDOM16.25
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]
-0.190.94-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.331
r_sphericity_free23.052
r_dihedral_angle_4_deg17.658
r_dihedral_angle_3_deg11.356
r_scangle_it11.033
r_sphericity_bonded9.848
r_scbond_it9.165
r_dihedral_angle_1_deg7.422
r_mcangle_it7.226
r_mcbond_it6.241
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.331
r_sphericity_free23.052
r_dihedral_angle_4_deg17.658
r_dihedral_angle_3_deg11.356
r_scangle_it11.033
r_sphericity_bonded9.848
r_scbond_it9.165
r_dihedral_angle_1_deg7.422
r_mcangle_it7.226
r_mcbond_it6.241
r_mcbond_other5.352
r_rigid_bond_restr5.066
r_angle_other_deg2.803
r_angle_refined_deg1.761
r_chiral_restr0.126
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_gen_planes_other0.005
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1814
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms50

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
Fcphasing