5KHP

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 1LM6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP296Acetate, Li2SO4, NaCl, ammonium Sulphate
Crystal Properties
Matthews coefficientSolvent content
3.0860.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.383α = 90
b = 114.383β = 90
c = 117.121γ = 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
12.655095.428.28.122217

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 REPLACEMENTTHROUGHOUT1LM62.655020976121995.320.208840.207740.22784RANDOM54.645
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]
0.20.2-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.479
r_dihedral_angle_3_deg15.531
r_dihedral_angle_4_deg14.08
r_long_range_B_refined9.623
r_long_range_B_other9.623
r_dihedral_angle_1_deg8.12
r_scangle_other6.703
r_mcangle_it5.707
r_mcangle_other5.706
r_scbond_it4.218
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.479
r_dihedral_angle_3_deg15.531
r_dihedral_angle_4_deg14.08
r_long_range_B_refined9.623
r_long_range_B_other9.623
r_dihedral_angle_1_deg8.12
r_scangle_other6.703
r_mcangle_it5.707
r_mcangle_other5.706
r_scbond_it4.218
r_scbond_other4.214
r_mcbond_it3.454
r_mcbond_other3.454
r_angle_refined_deg1.241
r_angle_other_deg0.891
r_chiral_restr0.047
r_gen_planes_refined0.015
r_bond_refined_d0.01
r_gen_planes_other0.008
r_bond_other_d0.004
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 Atoms4063
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms85

Software

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