4F2K

Macrophage Migration Inhibitory Factor covalently complexed with phenethylisothiocyanate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3L5VPDB ENTRY 3L5V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82981.9M (NH4)2SO4, 100mM Tris pH 8.0, 200mM NaCl, 4% v/v isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7755.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.728α = 90
b = 68.245β = 90
c = 88.715γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Osmic VariMax2011-10-13MSINGLE 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)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
11.5331.6481.40.057145.316301351308
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)
11.531.58140.3892.22.136220

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-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3L5V1.5331.646301351077255981.060.19020.19020.18830.2276RANDOM18.5078
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.786
r_dihedral_angle_4_deg16.248
r_dihedral_angle_3_deg10.348
r_dihedral_angle_1_deg5.769
r_scangle_it5.313
r_scbond_it3.464
r_angle_refined_deg2.193
r_mcangle_it2.071
r_mcbond_it1.294
r_chiral_restr0.165
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.786
r_dihedral_angle_4_deg16.248
r_dihedral_angle_3_deg10.348
r_dihedral_angle_1_deg5.769
r_scangle_it5.313
r_scbond_it3.464
r_angle_refined_deg2.193
r_mcangle_it2.071
r_mcbond_it1.294
r_chiral_restr0.165
r_bond_refined_d0.029
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2601
Nucleic Acid Atoms
Solvent Atoms343
Heterogen Atoms69

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling