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4-(2-isothiocyanatoethyl)benzenesulfonamide complexed with Macrophage Migration Inhibitory Factor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B1K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289.15 0.2 uL 11 mg/mL MIF (100 mM Tris-HCl pH 8.0, 200 mM NaCl) were mixed with 0.2 uL of reservoir solution. Sitting drop reservoir contained 33 uL of 2.0 M Ammonium sulfate, 0.1 M HEPES pH 7.0, 3% Isopropanol and <5mM 4-(2-isothiocyanatoethyl)benzenesulfonamide (10% DMSO final). Crystal was frozen in a solution of ~25% Glycerol, 75% reservoir
Crystal Properties Matthews coefficient Solvent content 3.79 67.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.333 α = 90 b = 96.333 β = 90 c = 104.957 γ = 120
Symmetry Space Group P 31 2 1
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 2024-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.954 Australian Synchrotron MX2
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 1.53 48.17 99.8 0.063 0.065 0.015 1 23.7 20 85163
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 1.53 1.56 96.4 2.311 2.378 0.552 0.554 17.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.53 48.17 1.34 85072 4312 99.78 0.1632 0.1625 0.1625 0.1777 0.1776
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 10.373 f_angle_d 1.092 f_chiral_restr 0.074 f_plane_restr 0.02 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2601 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 90
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing