5J7P

Macrophage Migration Inhibitory Factor bound to Covalent Inhibitor RDR03785


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293.152.2 M Ammonium Sulfate, 3% isopropanol and 0.1 M Tris pH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.6966.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.629α = 90
b = 95.629β = 90
c = 103.497γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2015-05-04MSINGLE 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
11.8582.821000.0890.0950.03311.57.847180
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)
11.851.881000.7410.8390.390.7054.52358

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 REPLACEMENTTHROUGHOUT3U181.8582.8242548458699.930.180.17780.2008RANDOM19.918
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]
-0.04-0.02-0.040.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.524
r_dihedral_angle_4_deg18.444
r_dihedral_angle_3_deg10.542
r_dihedral_angle_1_deg5.366
r_angle_refined_deg1.433
r_mcangle_it1.27
r_mcbond_it0.828
r_mcbond_other0.828
r_angle_other_deg0.719
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.524
r_dihedral_angle_4_deg18.444
r_dihedral_angle_3_deg10.542
r_dihedral_angle_1_deg5.366
r_angle_refined_deg1.433
r_mcangle_it1.27
r_mcbond_it0.828
r_mcbond_other0.828
r_angle_other_deg0.719
r_chiral_restr0.089
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2593
Nucleic Acid Atoms
Solvent Atoms251
Heterogen Atoms124

Software

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