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Crystal structure of macrophage migration inhibitory factor in complex with N-[3-(Trifluoromethyl)phenyl]-3-(2-chloroanilino)-2-cyano-3-thioxopropanamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DJH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20 mM Tris.HCl, pH 7.5, 2 M ammonium sulfate, and 3% 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.84 56.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.534 α = 90 b = 68.827 β = 90 c = 89.329 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 100 PIXEL DECTRIS PILATUS 200K 2014-05-13 M 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 1.63 50 99.8 0.034 26.4 3.6 53400
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 1.63 1.66 99.1 0.284 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.63 44.66 50632 2709 99.83 0.17118 0.16972 0.1832 0.19889 0.2095 RANDOM 19.759
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.386 r_dihedral_angle_4_deg 16.385 r_dihedral_angle_3_deg 10.452 r_dihedral_angle_1_deg 5.938 r_long_range_B_refined 4.992 r_long_range_B_other 4.618 r_angle_other_deg 3.769 r_scangle_other 3.55 r_scbond_it 2.542 r_scbond_other 2.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.386 r_dihedral_angle_4_deg 16.385 r_dihedral_angle_3_deg 10.452 r_dihedral_angle_1_deg 5.938 r_long_range_B_refined 4.992 r_long_range_B_other 4.618 r_angle_other_deg 3.769 r_scangle_other 3.55 r_scbond_it 2.542 r_scbond_other 2.541 r_mcangle_it 1.964 r_mcangle_other 1.964 r_angle_refined_deg 1.943 r_mcbond_it 1.498 r_mcbond_other 1.492 r_chiral_restr 0.166 r_gen_planes_other 0.028 r_bond_refined_d 0.022 r_gen_planes_refined 0.014 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2534 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction PHASER phasing PDB_EXTRACT data extraction HKL-2000 data scaling