4DNE

Crystal structure of a triple-mutant of streptavidin in complex with desthiobiotin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529310 mM MgSO4, 50 mM Na caodylate, 2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.72α = 90
b = 93.782β = 90
c = 104.413γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-09-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9334ESRFID14-1

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
11.885099.50.1216.1191931909712.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.9896.70.41

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1MK51.8846.86182301811996699.390.183230.183230.181410.21897RANDOM15.225
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]
0.530.01-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.774
r_dihedral_angle_4_deg13.899
r_dihedral_angle_3_deg12.371
r_dihedral_angle_1_deg6.935
r_scangle_it2.782
r_scbond_it1.857
r_mcangle_it1.397
r_angle_refined_deg1.382
r_mcbond_it0.765
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.774
r_dihedral_angle_4_deg13.899
r_dihedral_angle_3_deg12.371
r_dihedral_angle_1_deg6.935
r_scangle_it2.782
r_scbond_it1.857
r_mcangle_it1.397
r_angle_refined_deg1.382
r_mcbond_it0.765
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1809
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms60

Software

Software
Software NamePurpose
MxCuBEdata collection
MERLOTphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling