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Crystal Structure of the Uperin-3.5 peptide from Uperoleia mjobergii forming cross-alpha fibril
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Reservoir contained 0.1 M KSCN, 0.1 M MES 6.03 pH, 20 %v/v Jeff 600 with cryo-protection of 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 1.53 19.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 19.7 α = 90 b = 28.44 β = 106.95 c = 20.32 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 R 4M 2017-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 1.45 19.44 97 0.085 0.089 0.999 15.7 10.636 3777 21.604
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 1.45 1.49 94.7 0.601 0.648 0.908 2.72 7.568
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 AB INITIO PHASING THROUGHOUT 1.45 19.44 3398 378 97.24 0.189 0.185 0.186 0.2288 0.2288 RANDOM 14.461
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] -0.29 -0.03 -1.1 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.735 r_dihedral_angle_3_deg 15.579 r_dihedral_angle_4_deg 6.228 r_dihedral_angle_1_deg 4.162 r_angle_refined_deg 1.783 r_angle_other_deg 0.946 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.735 r_dihedral_angle_3_deg 15.579 r_dihedral_angle_4_deg 6.228 r_dihedral_angle_1_deg 4.162 r_angle_refined_deg 1.783 r_angle_other_deg 0.946 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 250 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 5
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction Arcimboldo phasing