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Macrophage migration inhibitory factor S61H/Y100H mutant complexed with three Zinc ions (Zn3-MIF(S61H/Y100H)-L)
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 293 2.0M ammonium sulfate, 20mM Tris-HCl buffer (pH 7.5), 3% isopropanol
Crystal Properties Matthews coefficient Solvent content 2.69 54.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.153 α = 90 b = 68.211 β = 90 c = 86.906 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 2022-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.2 48.22 99.9 0.057 0.996 12.6 5.6 126809
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 1.2 1.22 100 0.823 0.669 2.1
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 THROUGHOUT 1.2 48.212 126731 6378 99.892 0.156 0.1552 0.1737 0.1843 17.855
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] -0.075 -0.053 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.635 r_lrange_it 14.424 r_lrange_other 13.565 r_dihedral_angle_3_deg 10.525 r_scangle_it 10.03 r_scangle_other 10.028 r_scbond_it 7.58 r_scbond_other 7.578 r_dihedral_angle_2_deg 5.98 r_dihedral_angle_1_deg 5.657
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.635 r_lrange_it 14.424 r_lrange_other 13.565 r_dihedral_angle_3_deg 10.525 r_scangle_it 10.03 r_scangle_other 10.028 r_scbond_it 7.58 r_scbond_other 7.578 r_dihedral_angle_2_deg 5.98 r_dihedral_angle_1_deg 5.657 r_mcangle_other 4.578 r_mcangle_it 4.577 r_rigid_bond_restr 4.558 r_mcbond_it 3.534 r_mcbond_other 3.531 r_angle_refined_deg 1.855 r_angle_other_deg 0.636 r_nbd_refined 0.257 r_xyhbond_nbd_refined 0.224 r_symmetry_nbd_other 0.208 r_nbd_other 0.196 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.139 r_metal_ion_refined 0.137 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.088 r_symmetry_nbd_refined 0.027 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 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 391 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing