3HOF

Structure of macrophage migration inhibitory factor (MIF) with caffeic acid at 1.9A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CA7PDB entry 1CA7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29630-42.5% MPD_P1K_P3350 mix (MDL Morpheus screen), 0.1M buffer 1 mix (MDL morpheus screen), pH 5.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.5251.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.669α = 90
b = 67.988β = 90
c = 89.135γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315double Si 111 crystal monochromator2009-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9702DiamondI04

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
11.937.399.30.1098.44.433285924.8
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)
11.91.971000.2544.14.53

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 1CA71.932.2731196166399.30.174220.172830.19958RANDOM16.023
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]
-0.21-0.590.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.157
r_dihedral_angle_3_deg13.895
r_dihedral_angle_4_deg13.417
r_dihedral_angle_1_deg5.636
r_scangle_it3.835
r_scbond_it2.419
r_angle_refined_deg1.408
r_mcangle_it1.279
r_mcbond_it0.726
r_chiral_restr0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.157
r_dihedral_angle_3_deg13.895
r_dihedral_angle_4_deg13.417
r_dihedral_angle_1_deg5.636
r_scangle_it3.835
r_scbond_it2.419
r_angle_refined_deg1.408
r_mcangle_it1.279
r_mcbond_it0.726
r_chiral_restr0.116
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2662
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms13

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling