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S4 symmetric peptide design number 1, Tim zinc-bound form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 1.1 M sodium malonate, 0.1 M HEPES, pH 7, 0.5% (w/v) Jeffamine ED-2003
Crystal Properties Matthews coefficient Solvent content 1.95 36.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 20.96 α = 106.103 b = 20.98 β = 94.813 c = 26.88 γ = 89.429
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2018-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.729300 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 0.77 20.88 88.7 0.039 0.046 0.999 15.3 3.597 46103 7.559
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.77 0.79 77.2 0.236 0.283 0.962 3.95 3.244
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION AB INITIO PHASING FREE R-VALUE 0.77 20.001 46103 4610 88.789 0.127 0.1263 0.1267 0.1318 0.1323 8.627
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] -0.086 0.006 -0.031 0.049 -0.005 0.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 53.282 r_dihedral_angle_3_deg 8.12 r_dihedral_angle_1_deg 2.619 r_scangle_it 2.138 r_scangle_other 2.132 r_lrange_it 1.874 r_lrange_other 1.776 r_angle_refined_deg 1.594 r_scbond_it 1.552 r_scbond_other 1.546
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 53.282 r_dihedral_angle_3_deg 8.12 r_dihedral_angle_1_deg 2.619 r_scangle_it 2.138 r_scangle_other 2.132 r_lrange_it 1.874 r_lrange_other 1.776 r_angle_refined_deg 1.594 r_scbond_it 1.552 r_scbond_other 1.546 r_rigid_bond_restr 1.231 r_dihedral_angle_other_2_deg 1.017 r_mcangle_it 0.944 r_mcangle_other 0.94 r_mcbond_it 0.639 r_mcbond_other 0.638 r_angle_other_deg 0.499 r_nbd_refined 0.252 r_symmetry_nbd_other 0.238 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.147 r_nbd_other 0.115 r_chiral_restr 0.085 r_symmetry_nbd_refined 0.085 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_refined 0.055 r_metal_ion_refined 0.04 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 204 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction SHELXT phasing