Navigation Tabs Joint Xray/Neutron structure of Macrophage Migration Inhibitory Factor (MIF) Bound to 4-hydroxyphenylpyruvate at room temperature
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IJJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 295 Protein: 1 mM MIF, 10 mM deuterated HPP, 20 mM NaCl in 20 mM Tris (pH 7.4) mixed 1:1 with reservoir containing 2M (NH4)2SO4, 1% isopropanol in 100 mM Tris (pH 7.4).
Crystal Properties Matthews coefficient Solvent content 2.86 56.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.613 α = 90 b = 69.231 β = 90 c = 89.185 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 293 PIXEL DECTRIS EIGER R 4M 2017-07-10 M SINGLE WAVELENGTH 2 1 neutron 293 IMAGE PLATE MAATEL IMAGINE 2017-06-12 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54148 2 NUCLEAR REACTOR ORNL High Flux Isotope Reactor BEAMLINE CG4D 2.8-4.5 ORNL High Flux Isotope Reactor CG4D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.75 54.69 100 0.086 0.101 0.044 0.988 10.4 4.7 43601 22.02 2 2.5 17.62 80 0.251 0.269 0.092 0.948 5.7 5.9 11735 15.03
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 0.586 0.649 0.31 0.77 2.6 4.6 2 2.5 2.59 0.349 0.398 0.181 0.679 2.2 3.4
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS 1.75 54.69 1.36 43541 2136 100 0.1553 0.154 0.1555 0.1805 0.1832 22.55 NEUTRON DIFFRACTION FOURIER SYNTHESIS 2.53 17.62 11721 579 79.73 0.2214 0.2189 0.2705 22.55
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.4063 f_dihedral_angle_d 20.4063 f_angle_d 1.5703 f_angle_d 1.5703 f_bond_d 0.0976 f_bond_d 0.0976 f_chiral_restr 0.0794 f_chiral_restr 0.0794 f_plane_restr 0.0095 f_plane_restr 0.0095
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2601 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement
