3U18

Chicago Sky Blue 6B, A Novel Inhibitor for Macrophage Migration Inhibitory Factor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MIFpdb entry 1MIF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8310100 mM p425 dissolved in 2.0 M ammonium sulfate, 4% 2-propanol, 0.1 M Tris, VAPOR DIFFUSION, temperature 310K, pH 8
Crystal Properties
Matthews coefficientSolvent content
2.6954.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.857α = 90
b = 67.907β = 90
c = 86.572γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDOXFORD ONYX CCD2011-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOXFORD DIFFRACTION ENHANCE ULTRA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.8930.3499.70.06813.94.83264033
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)
11.891.9998.10.2084.42.5

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 1MIF1.930.3430441164999.620.142740.14090.17701RANDOM13.799
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]
0.03-0.120.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.532
r_dihedral_angle_4_deg18.95
r_dihedral_angle_3_deg12.296
r_dihedral_angle_1_deg5.612
r_angle_refined_deg2.337
r_chiral_restr0.183
r_bond_refined_d0.024
r_gen_planes_refined0.013
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.532
r_dihedral_angle_4_deg18.95
r_dihedral_angle_3_deg12.296
r_dihedral_angle_1_deg5.612
r_angle_refined_deg2.337
r_chiral_restr0.183
r_bond_refined_d0.024
r_gen_planes_refined0.013
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2601
Nucleic Acid Atoms
Solvent Atoms313
Heterogen Atoms156

Software

Software
Software NamePurpose
CrysalisProdata collection
PHASERphasing
REFMACrefinement
CrysalisProdata reduction
SCALAdata scaling