3IJG

Macrophage Migration Inhibitory Factor (MIF) Bound to the (R)-Stereoisomer of AV1013


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 with protein:inhibitor complex in a 1:1 ratio, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Crystal Properties
Matthews coefficientSolvent content
2.6854.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.958α = 90
b = 68.035β = 90
c = 87.279γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IVmirrors2009-01-12SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.710095.50.07319.24.342688-3
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)
1.71.73960.5143.72099

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3DJH1.710042564133295.50.1940.206random22.329
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]
0.4-1.9911.591
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it1.357
c_angle_deg1.29
c_mcbond_it1.103
c_mcangle_it0.991
c_scbond_it0.657
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2584
Nucleic Acid Atoms
Solvent Atoms389
Heterogen Atoms27

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling