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Structure characterization and anticancer potential of the fungal immunomodulatory protein FIP-ach
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KCW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.09 M NPS (0.3M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3M Ammonium sulfate),
0.1M buffer system 1 pH 6.5 (1M imidazole, 1M MES monohydrate)
30 % v/v Precipitant Mix 3 (40% v/v Glycerol; 20% w/v PEG 4000)
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.318 α = 90 b = 73.318 β = 90 c = 167.539 γ = 120
Symmetry Space Group P 31 2 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 EIGER2 X 16M 2023-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
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 2.13 50.6 99.8 0.061 0.999 15.7 11 29993
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.19 100 0.933 2.1 11.2
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 THROUGHOUT 2.13 50.6 29928 1526 99.757 0.231 0.2295 0.2299 0.266 0.2673 67.113
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] 2.333 1.166 2.333 -7.568
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.941 r_dihedral_angle_3_deg 15.166 r_dihedral_angle_2_deg 13.787 r_lrange_it 12.88 r_scangle_it 10.781 r_scbond_it 9.127 r_mcangle_it 8.83 r_dihedral_angle_1_deg 8.485 r_mcbond_it 6.848 r_angle_refined_deg 2.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.941 r_dihedral_angle_3_deg 15.166 r_dihedral_angle_2_deg 13.787 r_lrange_it 12.88 r_scangle_it 10.781 r_scbond_it 9.127 r_mcangle_it 8.83 r_dihedral_angle_1_deg 8.485 r_mcbond_it 6.848 r_angle_refined_deg 2.006 r_symmetry_xyhbond_nbd_refined 0.467 r_nbtor_refined 0.328 r_nbd_refined 0.243 r_symmetry_nbd_refined 0.193 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.127 r_gen_planes_refined 0.011 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1832 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing