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Crystal structure of Macrophage Migration Inhibitory Factor in complex with benzaldehyde
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 2.73 54.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.601 α = 90 b = 67.812 β = 90 c = 88.323 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++ 2013-11-20 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 1.63 50 98.7 0.029 26.5 4.7 50847
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 97.6 0.214 4.5 2481
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 42.09 50787 2581 98.69 0.1842 0.1825 0.1955 0.2136 0.2229 RANDOM 15.132
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 39.614 r_dihedral_angle_4_deg 17.054 r_dihedral_angle_3_deg 9.418 r_dihedral_angle_1_deg 5.989 r_angle_other_deg 4.71 r_mcangle_it 2.088 r_angle_refined_deg 2.087 r_mcbond_it 1.538 r_mcbond_other 1.538 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.614 r_dihedral_angle_4_deg 17.054 r_dihedral_angle_3_deg 9.418 r_dihedral_angle_1_deg 5.989 r_angle_other_deg 4.71 r_mcangle_it 2.088 r_angle_refined_deg 2.087 r_mcbond_it 1.538 r_mcbond_other 1.538 r_chiral_restr 0.124 r_gen_planes_other 0.026 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2522 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 46
Software Software Software Name Purpose HKL-2000 data reduction REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling PHASER phasing DENZO data reduction SCALEPACK data scaling