5N8J

CRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE D-amino acid containing peptide GyGlanvdessG


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1M Sodium citrate pH 5.6 20% PEG4000 20% Isopropanol

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.665α = 90
b = 84.878β = 99.1
c = 57.754γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.700002SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)CC (Half)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
11.0557.0999.60.0360.99911.43.43195681
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.051.1499.70.640.3881.113.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.0557.091956811021199.860.169820.168610.19308RANDOM16.321
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]
-0.33-0.260.040.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.597
r_sphericity_free23.05
r_dihedral_angle_4_deg13.681
r_dihedral_angle_3_deg11.002
r_dihedral_angle_1_deg6.955
r_sphericity_bonded5.148
r_long_range_B_refined2.287
r_long_range_B_other2.287
r_angle_refined_deg1.451
r_rigid_bond_restr1.236
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.597
r_sphericity_free23.05
r_dihedral_angle_4_deg13.681
r_dihedral_angle_3_deg11.002
r_dihedral_angle_1_deg6.955
r_sphericity_bonded5.148
r_long_range_B_refined2.287
r_long_range_B_other2.287
r_angle_refined_deg1.451
r_rigid_bond_restr1.236
r_scangle_other1.092
r_mcangle_it1.029
r_mcangle_other1.029
r_scbond_it0.931
r_scbond_other0.931
r_angle_other_deg0.89
r_mcbond_it0.801
r_mcbond_other0.799
r_chiral_restr0.091
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3767
Nucleic Acid Atoms
Solvent Atoms689
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SADABSdata scaling
PHASERphasing