3RDO

Crystal structure of R7-2 streptavidin complexed with biotin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RDMPDB ENTRY 3RDM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52980.1 M ammonium sulfate, 0.1 M Tris, pH 7.5, 20% PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3748.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.36α = 90
b = 57.36β = 90
c = 184.067γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9791NSLSX29A

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
11.45096.30.04816.75.829759
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)
11.41.4570.10.4882.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3RDM1.40419.2628218149597.170.151820.150820.17094RANDOM15.428
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.752
r_dihedral_angle_4_deg13.121
r_dihedral_angle_3_deg10.727
r_dihedral_angle_1_deg6.568
r_scbond_it3.534
r_mcangle_it2.506
r_scangle_it1.62
r_angle_refined_deg1.39
r_mcbond_it1.207
r_rigid_bond_restr0.713
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.752
r_dihedral_angle_4_deg13.121
r_dihedral_angle_3_deg10.727
r_dihedral_angle_1_deg6.568
r_scbond_it3.534
r_mcangle_it2.506
r_scangle_it1.62
r_angle_refined_deg1.39
r_mcbond_it1.207
r_rigid_bond_restr0.713
r_chiral_restr0.087
r_bond_refined_d0.008
r_gen_planes_refined0.005
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms951
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms34

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction