5KID

Tightening the Recognition of Tetravalent Zr and Th Complexes by the Siderophore-Binding Mammalian Protein Siderocalin for Theranostic Applications


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L6M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298NaCl,Li2SO4,Acetate, Ammonium Sulphate
Crystal Properties
Matthews coefficientSolvent content
3.261.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.547α = 90
b = 115.547β = 90
c = 118.028γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.0ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.155096.825.78.342554

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 REPLACEMENTTHROUGHOUT1L6M2.155039580201794.730.233760.232290.26343RANDOM58.963
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]
-0.69-0.691.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.458
r_dihedral_angle_4_deg16.051
r_dihedral_angle_3_deg13.92
r_dihedral_angle_1_deg6.725
r_long_range_B_refined5.708
r_long_range_B_other5.707
r_scangle_other3.318
r_mcangle_it2.492
r_mcangle_other2.492
r_scbond_it2.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.458
r_dihedral_angle_4_deg16.051
r_dihedral_angle_3_deg13.92
r_dihedral_angle_1_deg6.725
r_long_range_B_refined5.708
r_long_range_B_other5.707
r_scangle_other3.318
r_mcangle_it2.492
r_mcangle_other2.492
r_scbond_it2.154
r_scbond_other2.149
r_mcbond_it1.695
r_mcbond_other1.692
r_angle_refined_deg1.62
r_angle_other_deg0.986
r_chiral_restr0.101
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4111
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing