8SON

Crystal structure of macrophage migration inhibitory factor in complex with N-[3-(Trifluoromethyl)phenyl]-3-(2-chloroanilino)-2-cyano-3-thioxopropanamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DJH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529320 mM Tris.HCl, pH 7.5, 2 M ammonium sulfate, and 3% 2-propanol
Crystal Properties
Matthews coefficientSolvent content
2.8456.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.534α = 90
b = 68.827β = 90
c = 89.329γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2014-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.635099.80.03426.43.653400
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.631.6699.10.2843.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6344.6650632270999.830.171180.169720.19889RANDOM19.759
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.386
r_dihedral_angle_4_deg16.385
r_dihedral_angle_3_deg10.452
r_dihedral_angle_1_deg5.938
r_long_range_B_refined4.992
r_long_range_B_other4.618
r_angle_other_deg3.769
r_scangle_other3.55
r_scbond_it2.542
r_scbond_other2.541
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.386
r_dihedral_angle_4_deg16.385
r_dihedral_angle_3_deg10.452
r_dihedral_angle_1_deg5.938
r_long_range_B_refined4.992
r_long_range_B_other4.618
r_angle_other_deg3.769
r_scangle_other3.55
r_scbond_it2.542
r_scbond_other2.541
r_mcangle_it1.964
r_mcangle_other1.964
r_angle_refined_deg1.943
r_mcbond_it1.498
r_mcbond_other1.492
r_chiral_restr0.166
r_gen_planes_other0.028
r_bond_refined_d0.022
r_gen_planes_refined0.014
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 AtomsNumber
Protein Atoms2534
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms85

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling