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Fibrillar assembly of an D-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2N1E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.4-0.6 M sodium potassium phosphate, pH 7.0, 26% v/v PEG400, 2-12 mM I3C (5-amino-2,4,6-triiodoisphthalic acid)
Crystal Properties Matthews coefficient Solvent content 2.54 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.475 α = 90 b = 57.475 β = 90 c = 113.575 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 PIXEL DECTRIS EIGER X 16M 2022-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.92 50 99.3 0.167 0.174 0.045 1 39.5 19.2 15438
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 1.92 1.95 92 0.643 0.662 0.149 0.921 18.9
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 1.92 40.43 13671 692 93.97 0.24791 0.24556 0.2469 0.29613 0.2913 RANDOM 28.035
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] -0.39 -0.39 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.431 r_long_range_B_refined 8.218 r_long_range_B_other 8.155 r_dihedral_angle_1_deg 7.851 r_scangle_other 5.407 r_scbond_it 3.62 r_mcangle_other 3.59 r_mcangle_it 3.589 r_scbond_other 3.577 r_mcbond_it 2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.431 r_long_range_B_refined 8.218 r_long_range_B_other 8.155 r_dihedral_angle_1_deg 7.851 r_scangle_other 5.407 r_scbond_it 3.62 r_mcangle_other 3.59 r_mcangle_it 3.589 r_scbond_other 3.577 r_mcbond_it 2.45 r_mcbond_other 2.448 r_angle_refined_deg 1.859 r_angle_other_deg 0.453 r_chiral_restr 0.068 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 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 1212 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing