6CBF

Macrophage Migration Inhibitory Factor in Complex with a Pyrazole Inhibitor (6a)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52932.4M ammonium sulfate, 3% isopropanol, 0.1M Tris pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.6253.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.305α = 90
b = 68.31β = 90
c = 83.309γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2014-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.352.829716.236.417430
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.36

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.352.8214279160888.60.237370.232290.28192RANDOM33.646
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]
-0.71-0.981.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.391
r_dihedral_angle_4_deg14.812
r_dihedral_angle_3_deg13.766
r_dihedral_angle_1_deg5.733
r_long_range_B_refined4.695
r_long_range_B_other4.694
r_mcangle_other2.482
r_mcangle_it2.48
r_scangle_other2.371
r_mcbond_it1.455
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.391
r_dihedral_angle_4_deg14.812
r_dihedral_angle_3_deg13.766
r_dihedral_angle_1_deg5.733
r_long_range_B_refined4.695
r_long_range_B_other4.694
r_mcangle_other2.482
r_mcangle_it2.48
r_scangle_other2.371
r_mcbond_it1.455
r_mcbond_other1.45
r_scbond_it1.399
r_scbond_other1.377
r_angle_refined_deg1.344
r_angle_other_deg0.929
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2597
Nucleic Acid Atoms
Solvent Atoms18
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing