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Macrophage migration inhibitory factor Y100H mutant complexed with three Zinc ions (Zn3-MIF(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 2.72 54.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.906 α = 90 b = 68.32 β = 90 c = 87.629 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 EIGER2 XE 16M 2022-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 1.25 48.16 100 0.046 1 23.6 13.8 113184
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 1.25 1.27 1.017 0.842 2.7
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 1.25 48.16 113094 5571 99.995 0.119 0.1177 0.1227 0.1463 0.151 18.42
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] 0.171 -0.139 -0.031
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.907 r_dihedral_angle_6_deg 17.042 r_lrange_other 15.758 r_dihedral_angle_3_deg 11.862 r_scangle_it 11.004 r_scangle_other 11.001 r_dihedral_angle_2_deg 9.261 r_scbond_it 8.224 r_scbond_other 8.221 r_dihedral_angle_1_deg 5.671
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.907 r_dihedral_angle_6_deg 17.042 r_lrange_other 15.758 r_dihedral_angle_3_deg 11.862 r_scangle_it 11.004 r_scangle_other 11.001 r_dihedral_angle_2_deg 9.261 r_scbond_it 8.224 r_scbond_other 8.221 r_dihedral_angle_1_deg 5.671 r_mcangle_it 5.583 r_mcangle_other 5.583 r_mcbond_it 4.26 r_mcbond_other 4.258 r_rigid_bond_restr 4.206 r_angle_refined_deg 1.806 r_angle_other_deg 0.664 r_xyhbond_nbd_refined 0.285 r_nbd_refined 0.244 r_nbd_other 0.237 r_symmetry_xyhbond_nbd_refined 0.217 r_symmetry_nbd_other 0.195 r_symmetry_nbd_refined 0.185 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_other 0.136 r_chiral_restr 0.108 r_metal_ion_refined 0.101 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_chiral_restr_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2595 Nucleic Acid Atoms Solvent Atoms 529 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing