4XX7

Crystal structure of M2A mutant of human macrophage migration inhibitory factor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2912 M ammonium Sulphate, 3% 2-propanol, 20 mM Tris.HCl, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.7354.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.829α = 90
b = 68.153β = 90
c = 87.062γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2015-01-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.775098.50.0540.0560.01522.214.339379
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)
11.771.896.70.3250.3380.090.9713.41898

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 REPLACEMENTTHROUGHOUT3DJH1.7743.5337372194898.380.1610.15960.1868RANDOM18.534
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.868
r_dihedral_angle_4_deg20.336
r_dihedral_angle_3_deg11.369
r_dihedral_angle_1_deg5.444
r_angle_other_deg2.267
r_mcangle_it2.094
r_angle_refined_deg1.975
r_mcbond_it1.612
r_mcbond_other1.59
r_chiral_restr0.134
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.868
r_dihedral_angle_4_deg20.336
r_dihedral_angle_3_deg11.369
r_dihedral_angle_1_deg5.444
r_angle_other_deg2.267
r_mcangle_it2.094
r_angle_refined_deg1.975
r_mcbond_it1.612
r_mcbond_other1.59
r_chiral_restr0.134
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d0.009
r_gen_planes_other0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2533
Nucleic Acid Atoms
Solvent Atoms288
Heterogen Atoms29

Software

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