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Interactions between Pex3 and Pex19 peptide in yeast
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 ammonium phosphate 0.2M + PEG 3350 20%, ph 7.0
Crystal Properties Matthews coefficient Solvent content 2.58 52.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.579 α = 90 b = 137.224 β = 90 c = 111.534 γ = 90
Symmetry Space Group C 2 2 21
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 2023-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97624 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.62 111.53 100 0.101 0.111 0.045 0.999 11 11.4 16218
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 2.62 2.74 4.759 5.184 2.048 0.394 12.2
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.62 68.612 16197 844 99.932 0.211 0.2094 0.2097 0.2477 0.2493 110.698
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] 5.35 -0.837 -4.513
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 22.219 r_lrange_other 22.218 r_dihedral_angle_2_deg 18.585 r_scangle_it 17.908 r_scangle_other 17.904 r_dihedral_angle_3_deg 14.553 r_dihedral_angle_6_deg 14.388 r_mcangle_it 12.697 r_mcangle_other 12.694 r_scbond_it 12.35
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 22.219 r_lrange_other 22.218 r_dihedral_angle_2_deg 18.585 r_scangle_it 17.908 r_scangle_other 17.904 r_dihedral_angle_3_deg 14.553 r_dihedral_angle_6_deg 14.388 r_mcangle_it 12.697 r_mcangle_other 12.694 r_scbond_it 12.35 r_scbond_other 12.348 r_mcbond_it 9.213 r_mcbond_other 9.21 r_dihedral_angle_1_deg 4.818 r_angle_refined_deg 1.631 r_angle_other_deg 0.541 r_nbd_other 0.237 r_nbd_refined 0.233 r_nbtor_refined 0.186 r_symmetry_nbd_other 0.18 r_xyhbond_nbd_refined 0.116 r_symmetry_xyhbond_nbd_refined 0.111 r_symmetry_nbd_refined 0.101 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2713 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building