☰ Navigation Tabs
X-ray structure of Macrophage Migration Inhibitory Factor (MIF) Covalently Bound to 4-hydroxyphenylpyruvate (HPP)
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 7.5 293 2M AMMONIUM SULFATE, 4% ISOPROPANOL, 0.1 M TRIS(HYDROXYMETHYL)AMINOMETHAN; MIXED WITH PROTEIN:INHIBITOR COMPLEX IN A 1:10 RATIO
Crystal Properties Matthews coefficient Solvent content 2.82 56.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.57 α = 90 b = 68.87 β = 90 c = 88.43 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 CMOS RDI CMOS_8M 2018-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0 ALS 4.2.2
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 1.68 44.22 100 0.076 0.085 0.04 0.998 16.1 7.6 48464 28.05
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 1.68 1.71 100 2.208 2.426 1.302 0.314 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.68 44.22 0.31 48298 2346 99.73 0.1717 0.1703 0.1992 0.1918 33.87
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 15.6625 f_angle_d 1.3355 f_chiral_restr 0.092 f_bond_d 0.0144 f_plane_restr 0.0096
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2563 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 47
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling pointless data scaling PHASER phasing