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Macrophage Migration Inhibitory Factor 2 from Heligmosomoides polygyrus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296.15 0.8 M Na2 Succ (Precipitant)
Crystal Properties Matthews coefficient Solvent content 2.55 51.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.631 α = 90 b = 67.631 β = 90 c = 46.946 γ = 120
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 9M 2025-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.919716 NSLS-II 17-ID-1
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 1.396 29.302 100 0.113 0.116 0.026 0.999 15.514 20.13 24398
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 1.396 1.42 100 1.761 1.822 0.467 0.3479 1.417 15.11
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.396 29.302 24382 1199 99.984 0.151 0.149 0.176 0.1796 20
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] -0.052 -0.026 -0.052 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.067 r_dihedral_angle_3_deg 13.971 r_lrange_it 10.953 r_lrange_other 10.691 r_dihedral_angle_2_deg 10.206 r_scangle_it 7.891 r_scangle_other 7.884 r_dihedral_angle_1_deg 6.312 r_mcangle_it 5.929 r_mcangle_other 5.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.067 r_dihedral_angle_3_deg 13.971 r_lrange_it 10.953 r_lrange_other 10.691 r_dihedral_angle_2_deg 10.206 r_scangle_it 7.891 r_scangle_other 7.884 r_dihedral_angle_1_deg 6.312 r_mcangle_it 5.929 r_mcangle_other 5.925 r_scbond_it 5.396 r_scbond_other 5.39 r_rigid_bond_restr 4.127 r_mcbond_it 4.069 r_mcbond_other 4.067 r_angle_refined_deg 1.66 r_angle_other_deg 0.567 r_symmetry_nbd_refined 0.284 r_nbd_refined 0.223 r_nbd_other 0.194 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.17 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.081 r_chiral_restr_other 0.022 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 858 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction