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Macrophage Migration Inhibitory Factor (MIF) with Covalently Bound L-sulforaphane
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DJH PDB ebtry 3DJH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2 M ammonium sulfate, 3% isopropanol, 0.1
M tris(hydroxymethyl)aminomethane; mixed with protein:inhibitor complex in a 1:1 ratio, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.69 66.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.638 α = 90 b = 95.638 β = 90 c = 103.516 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 113 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2010-08-13 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 110 99.9 0.104 14.7 10.8 51163 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 100 0.502 4.2 10.4 2534
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ebtry 3DJH 1.8 110 51159 50929 1051 99.6 0.1722 0.178 0.1863 0.1899 random 16.2973
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] -0.572 -0.572 1.144
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_deg 24.4 c_angle_deg 1.3 c_improper_angle_deg 0.82 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2586 Nucleic Acid Atoms Solvent Atoms 446 Heterogen Atoms 43
Software Software Software Name Purpose AMoRE phasing CNS refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling