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Macrophage Migration Inhibitory Factor 2 from Necator americanus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MIF Monomer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 1.26 M NaH2PO4 (Precipitant), 0.14 M K2HPO4 (Precipitant)
Crystal Properties Matthews coefficient Solvent content 2.88 57.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.653 α = 90 b = 64.653 β = 90 c = 174.687 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 16M 2024-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979338 NSLS-II 17-ID-2
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 1.726 29.115 92.3 0.052 0.057 0.024 0.999 12.7 5.71 14008
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 1.726 1.756 100 1.685 1.861 0.774 0.446 0.8 5.56
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.726 29.115 13917 683 91.68 0.192 0.1912 0.2088 0.2422 Random 47
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] -0.479 -0.239 -0.479 1.553
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.249 r_lrange_other 19.203 r_scangle_it 15.168 r_scangle_other 15.155 r_dihedral_angle_3_deg 15.085 r_dihedral_angle_6_deg 13.499 r_mcangle_it 12.235 r_mcangle_other 12.234 r_scbond_it 10.721 r_scbond_other 10.708
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.249 r_lrange_other 19.203 r_scangle_it 15.168 r_scangle_other 15.155 r_dihedral_angle_3_deg 15.085 r_dihedral_angle_6_deg 13.499 r_mcangle_it 12.235 r_mcangle_other 12.234 r_scbond_it 10.721 r_scbond_other 10.708 r_mcbond_it 9.269 r_mcbond_other 9.266 r_dihedral_angle_2_deg 8.268 r_dihedral_angle_1_deg 6.402 r_rigid_bond_restr 4.752 r_angle_refined_deg 1.731 r_angle_other_deg 0.571 r_nbd_other 0.268 r_nbd_refined 0.229 r_symmetry_nbd_refined 0.226 r_symmetry_nbd_other 0.206 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.147 r_symmetry_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.059 r_chiral_restr_other 0.024 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 843 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing Coot model building