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Tightening the Recognition of Tetravalent Zr and Th Complexes by the Siderophore-Binding Mammalian Protein Siderocalin for Theranostic Applications
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L6M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 NaCl,Li2SO4,Acetate, Ammonium Sulphate
Crystal Properties Matthews coefficient Solvent content 3.2 61.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.547 α = 90 b = 115.547 β = 90 c = 118.028 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2015-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.15 50 96.8 25.7 8.3 42554
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1L6M 2.15 50 39580 2017 94.73 0.23376 0.23229 0.26343 0.2839 RANDOM 58.963
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 -0.69 1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.458 r_dihedral_angle_4_deg 16.051 r_dihedral_angle_3_deg 13.92 r_dihedral_angle_1_deg 6.725 r_long_range_B_refined 5.708 r_long_range_B_other 5.707 r_scangle_other 3.318 r_mcangle_it 2.492 r_mcangle_other 2.492 r_scbond_it 2.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.458 r_dihedral_angle_4_deg 16.051 r_dihedral_angle_3_deg 13.92 r_dihedral_angle_1_deg 6.725 r_long_range_B_refined 5.708 r_long_range_B_other 5.707 r_scangle_other 3.318 r_mcangle_it 2.492 r_mcangle_other 2.492 r_scbond_it 2.154 r_scbond_other 2.149 r_mcbond_it 1.695 r_mcbond_other 1.692 r_angle_refined_deg 1.62 r_angle_other_deg 0.986 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 4111 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing