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X-ray Structure of a Second-Sphere H-bond Deletion Mutant of a De Novo Designed Self Assembled Peptide Tetramer Featuring a Cu(His)4(H2O) Coordination Motif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8VHS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 0.1M Tris pH 8.5,
0.2M MgCl2.6H2O,
28% PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.95 37.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.553 α = 90 b = 45.309 β = 98.54 c = 40.524 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 16M 2024-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97936 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.47 28.15 98.2 0.07 0.998 11.9 6.8 20743
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.51 0.49 0.97
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 (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 1.47 28.15 19729 1009 98.18 0.2049 0.20337 0.2152 0.23624 0.245 RANDOM 31.232
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] 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.871 r_long_range_B_other 11.795 r_long_range_B_refined 11.719 r_scangle_other 7.006 r_dihedral_angle_1_deg 5.434 r_mcangle_it 5.205 r_mcangle_other 5.202 r_scbond_it 4.371 r_scbond_other 4.368 r_mcbond_it 3.537
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.871 r_long_range_B_other 11.795 r_long_range_B_refined 11.719 r_scangle_other 7.006 r_dihedral_angle_1_deg 5.434 r_mcangle_it 5.205 r_mcangle_other 5.202 r_scbond_it 4.371 r_scbond_other 4.368 r_mcbond_it 3.537 r_mcbond_other 3.464 r_angle_refined_deg 1.848 r_angle_other_deg 0.65 r_chiral_restr 0.093 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg 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 1130 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing