3SMC

Macrophage Migration Inhibitory Factor (MIF) with Covalently Bound L-sulforaphane


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52932 M ammonium sulfate, 3% isopropanol, 0.1 M tris(hydroxymethyl)aminomethane; mixed with protein:inhibitor complex in a 1:1 ratio, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6966.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.638α = 90
b = 95.638β = 90
c = 103.516γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU RAXIS IV++mirrors2010-08-13SINGLE 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
11.811099.90.10414.710.851163-3
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)
11.81.831000.5024.210.42534

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ebtry 3DJH1.81105115950929105199.60.17220.1863random16.2973
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]
-0.572-0.5721.144
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_deg24.4
c_angle_deg1.3
c_improper_angle_deg0.82
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2586
Nucleic Acid Atoms
Solvent Atoms446
Heterogen Atoms43

Software

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