5J7Q

Macrophage Migration Inhibitory Factor bound to Inhibitor K664 Derivative


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3U18 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293.152.4 M Ammonium Sulfate, 3% isopropanol and 0.1 M Tris pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.7354.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.699α = 90
b = 67.732β = 90
c = 88.152γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2015-07-15MSINGLE 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)Rrim I (All)Rpim I (All)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
11.9553.7198.60.0880.0950.0376.46.329961
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.951.9893.40.8570.9830.4780.61841376

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 REPLACEMENTTHROUGHOUT3U182.0553.7123028256697.430.19910.19540.233RANDOM27.31
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]
-0.15-0.460.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.513
r_dihedral_angle_4_deg18.699
r_dihedral_angle_3_deg11.852
r_dihedral_angle_1_deg5.49
r_mcangle_it2.18
r_mcbond_it1.482
r_mcbond_other1.481
r_angle_refined_deg1.47
r_angle_other_deg0.786
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.513
r_dihedral_angle_4_deg18.699
r_dihedral_angle_3_deg11.852
r_dihedral_angle_1_deg5.49
r_mcangle_it2.18
r_mcbond_it1.482
r_mcbond_other1.481
r_angle_refined_deg1.47
r_angle_other_deg0.786
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2599
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms68

Software

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