6CBG

Macrophage Migration Inhibitory Factor in Complex with a Pyrazole Inhibitor (5)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WRB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293.152.4M ammonium sulfate, 3% isopropanol, 0.1M Tris pH 7
Crystal Properties
Matthews coefficientSolvent content
2.7354.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.331α = 90
b = 68.258β = 90
c = 86.753γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2014-07-19MSINGLE 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
1253.6897.9249.233.124739
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.05

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 REPLACEMENTTHROUGHOUT4wrb253.6824739276497.920.17150.167810.20474RANDOM15.416
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]
-0.350.10.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.236
r_dihedral_angle_4_deg20.533
r_dihedral_angle_3_deg10.75
r_dihedral_angle_1_deg5.402
r_long_range_B_refined3.932
r_long_range_B_other3.931
r_scangle_other1.864
r_angle_refined_deg1.402
r_scbond_it1.197
r_scbond_other1.197
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.236
r_dihedral_angle_4_deg20.533
r_dihedral_angle_3_deg10.75
r_dihedral_angle_1_deg5.402
r_long_range_B_refined3.932
r_long_range_B_other3.931
r_scangle_other1.864
r_angle_refined_deg1.402
r_scbond_it1.197
r_scbond_other1.197
r_mcangle_it1.043
r_mcangle_other1.043
r_angle_other_deg0.909
r_mcbond_it0.656
r_mcbond_other0.656
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 Atoms2571
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms112

Software

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