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Crystal Structure of a de Novo Three-stranded Coiled Coil Peptide Containing Trigonal Pyrmidal Pb(II) complexes in the dual Tris-thiolate Site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EGL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 293 40% (v/v) PEG-400, sodium acetate buffer pH 4.5 at a final well solution pH 5.4
Crystal Properties Matthews coefficient Solvent content 2.39 48.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.13 α = 90 b = 38.13 β = 90 c = 139.957 γ = 120
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 MARMOSAIC 225 mm CCD 2018-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.29 50 99.7 0.061 0.063 0.016 10.6 15.4 10269 17.11
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.29 1.31 100 0.562 0.581 0.148 0.976 15.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6EGL 1.29 24.02 10267 507 99.8 0.164 0.164 0.1733 0.172 0.1894 RANDOM 26.5
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] -2.9376 -2.9376 5.8752
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.96 t_omega_torsion 2.17 t_angle_deg 1.12 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.96 t_omega_torsion 2.17 t_angle_deg 1.12 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 285 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 5
Software Software Software Name Purpose BUSTER refinement HKL-2000 data reduction SCALEPACK data scaling PDB_EXTRACT data extraction MOLREP phasing