5HVS

Crystal Structure of Macrophage Migration Inhibitory Factor (MIF) with a Biaryltriazole Inhibitor (3i-305)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3U18 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293.152.0M ammonium sulfate, 0.1M Tris-HCl pH 8, 3% isopropanol
Crystal Properties
Matthews coefficientSolvent content
2.1642.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.531α = 90
b = 69.744β = 90
c = 133.793γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2015-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.755099.20.0540.0610.02921.83.532486
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)
11.751.7896.70.1752

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT3U181.755029385328199.580.17370.17010.2056RANDOM18.721
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]
0.13-0.140.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.436
r_dihedral_angle_4_deg18.473
r_dihedral_angle_3_deg11.322
r_dihedral_angle_1_deg5.083
r_angle_refined_deg1.497
r_mcangle_it1.155
r_mcbond_it0.774
r_mcbond_other0.774
r_angle_other_deg0.765
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.436
r_dihedral_angle_4_deg18.473
r_dihedral_angle_3_deg11.322
r_dihedral_angle_1_deg5.083
r_angle_refined_deg1.497
r_mcangle_it1.155
r_mcbond_it0.774
r_mcbond_other0.774
r_angle_other_deg0.765
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2599
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms141

Software

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