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Macrophage migration inhibitory factor S61H/Y100H mutant complexed with three Zinc ions (Zn3-MIF(S61H/Y100H))
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DJH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2.0M ammonium sulfate, 20mM Tris-HCl buffer (pH 7.5), 3% isopropanol
Crystal Properties Matthews coefficient Solvent content 2.71 54.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.35 α = 90 b = 68.609 β = 90 c = 86.785 γ = 90
Symmetry Space Group P 21 21 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 2024-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0 SPring-8 BL45XU
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 1.3 48.42 100 0.097 0.995 10.8 6.8 100854
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 0.923 0.729 2.2
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 1.3 48.42 100771 5096 99.996 0.138 0.1369 0.1426 0.1673 0.1731 14.52
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] -0.042 0.052 -0.01
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.059 r_dihedral_angle_6_deg 16.69 r_lrange_other 15.175 r_dihedral_angle_3_deg 10.274 r_scangle_it 9.143 r_scangle_other 9.141 r_dihedral_angle_2_deg 7.222 r_scbond_it 6.91 r_scbond_other 6.908 r_dihedral_angle_1_deg 5.842
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.059 r_dihedral_angle_6_deg 16.69 r_lrange_other 15.175 r_dihedral_angle_3_deg 10.274 r_scangle_it 9.143 r_scangle_other 9.141 r_dihedral_angle_2_deg 7.222 r_scbond_it 6.91 r_scbond_other 6.908 r_dihedral_angle_1_deg 5.842 r_mcangle_other 4.419 r_mcangle_it 4.418 r_rigid_bond_restr 4.414 r_mcbond_it 3.396 r_mcbond_other 3.392 r_angle_refined_deg 1.825 r_angle_other_deg 0.673 r_symmetry_xyhbond_nbd_other 0.421 r_symmetry_xyhbond_nbd_refined 0.389 r_symmetry_nbd_refined 0.278 r_xyhbond_nbd_refined 0.248 r_nbd_refined 0.24 r_nbd_other 0.235 r_symmetry_nbd_other 0.208 r_nbtor_refined 0.174 r_chiral_restr 0.107 r_metal_ion_refined 0.084 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2607 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing