3IJJ

Ternary Complex of Macrophage Migration Inhibitory Factor (MIF) Bound Both to 4-hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-stereoisomer)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.53102 M ammonium sulfate, 3% isopropanol, 0.5 M NaCl, 0.1 M tris(hydroxymethyl)aminomethane; mixed in a 1:1 ratio with the protein:substrate:inhibitor complex, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Crystal Properties
Matthews coefficientSolvent content
2.6954.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.236α = 90
b = 67.908β = 90
c = 87.329γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirror and monochromator2009-06-17SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.081NSLSX29A

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
11.2510099.90.06416.94.8110659-3
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)
1.251.271000.4754.75484

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 REPLACEMENTTHROUGHOUTPDB Entry 3DJH1.2553.61110630111799.750.1630.1620.185RANDOM16.909
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]
-0.040.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.216
r_dihedral_angle_4_deg13.832
r_dihedral_angle_3_deg10.37
r_scangle_it7.036
r_dihedral_angle_1_deg5.203
r_scbond_it4.848
r_mcangle_it3.842
r_mcbond_it2.463
r_rigid_bond_restr1.695
r_angle_refined_deg1.201
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.216
r_dihedral_angle_4_deg13.832
r_dihedral_angle_3_deg10.37
r_scangle_it7.036
r_dihedral_angle_1_deg5.203
r_scbond_it4.848
r_mcangle_it3.842
r_mcbond_it2.463
r_rigid_bond_restr1.695
r_angle_refined_deg1.201
r_chiral_restr0.079
r_gen_planes_refined0.031
r_bond_refined_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2570
Nucleic Acid Atoms
Solvent Atoms479
Heterogen Atoms103

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling