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Crystal Structure of Macrophage Migration Inhibitory Factor (MIF) with a Potent Inhibitor (NVS-2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OOH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 2.0 M Ammonium Sulfate, 3% isopropanol and 0.1 M Tris pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.74 67.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.023 α = 90 b = 96.023 β = 90 c = 104.039 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 CCD RIGAKU SATURN 944+ 2015-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (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 83.16 100 0.086 0.092 0.032 15.3 7.1 56173
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 1.75 1.78 99.9 0.795 0.919 0.457 0.646 4 2741
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2OOH 1.75 83.16 50398 5644 99.72 0.1798 0.1773 0.2027 0.1896 RANDOM 20.916
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] -0.07 -0.03 -0.07 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.458 r_dihedral_angle_4_deg 17.459 r_dihedral_angle_3_deg 12.055 r_dihedral_angle_1_deg 5.636 r_mcangle_it 1.514 r_angle_refined_deg 1.407 r_mcbond_it 1.043 r_mcbond_other 1.041 r_angle_other_deg 0.954 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.458 r_dihedral_angle_4_deg 17.459 r_dihedral_angle_3_deg 12.055 r_dihedral_angle_1_deg 5.636 r_mcangle_it 1.514 r_angle_refined_deg 1.407 r_mcbond_it 1.043 r_mcbond_other 1.041 r_angle_other_deg 0.954 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2589 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing