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Crystal Structure Analysis of Macrophage Migration Inhibitory Factor in complex with N-[(4-cyanophenyl)methyl]methanethioamide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 2 M ammonium Sulphate, 3% 2-propanol, 20 mM Tris.HCl, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.76 55.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.144 α = 90 b = 68.386 β = 90 c = 87.685 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 93 IMAGE PLATE RIGAKU RAXIS IV++ 2013-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 2.07 50 99.6 0.065 10.9 4.4 25650
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 2.07 25.07 25499 1303 99.22 0.1877 0.1856 0.1989 0.2275 0.2374 RANDOM 25.562
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.84 r_dihedral_angle_4_deg 21.577 r_dihedral_angle_3_deg 11.871 r_dihedral_angle_1_deg 6.074 r_mcangle_it 3.085 r_mcbond_it 2.252 r_mcbond_other 2.244 r_angle_refined_deg 1.796 r_angle_other_deg 1.756 r_chiral_restr 0.167
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.84 r_dihedral_angle_4_deg 21.577 r_dihedral_angle_3_deg 11.871 r_dihedral_angle_1_deg 6.074 r_mcangle_it 3.085 r_mcbond_it 2.252 r_mcbond_other 2.244 r_angle_refined_deg 1.796 r_angle_other_deg 1.756 r_chiral_restr 0.167 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2502 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 41
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing HKL-2000 data reduction Crystal data reduction DENZO data reduction SCALEPACK data scaling