6S4Q

scdSav(SASK) - Engineering Single-Chain Dimeric Streptavidin as Host for Artificial Metalloenzymes


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PK2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42932 M (NH4)2SO4, 0.1 M Na-Acetate, pH 4
Crystal Properties
Matthews coefficientSolvent content
2.7955.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 184.219α = 90
b = 57.201β = 108.09
c = 57.201γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2018-09-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.8543.821000.1020.99783.354365
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8999.91.0970.4311.23.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3PK21.8543.8248458288799.630.1950.231RANDOM30.558
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]
2.080.75-1.42-0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.046
r_dihedral_angle_4_deg20.24
r_dihedral_angle_3_deg14.452
r_dihedral_angle_1_deg8.009
r_mcangle_it4.229
r_angle_refined_deg2.945
r_mcbond_it2.854
r_mcbond_other2.854
r_angle_other_deg2.552
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.046
r_dihedral_angle_4_deg20.24
r_dihedral_angle_3_deg14.452
r_dihedral_angle_1_deg8.009
r_mcangle_it4.229
r_angle_refined_deg2.945
r_mcbond_it2.854
r_mcbond_other2.854
r_angle_other_deg2.552
r_chiral_restr0.077
r_bond_other_d0.038
r_gen_planes_other0.015
r_bond_refined_d0.011
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3633
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms358

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing