6BG7

Crystal structure of G107A 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 DROP7.52932 M ammonium sulfate, 3% 2-propanol, 0.1 M Tris-HCl, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.7166.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.863α = 90
b = 95.863β = 90
c = 103.712γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2017-10-02MSINGLE 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
12.545083.70.0820.0990.0548.22.615576
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)
12.552.59830.3840.4760.2740.8122.4

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 REPLACEMENTTHROUGHOUT3DJH2.5447.931469875883.010.19980.19840.2254RANDOM35.66
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]
-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.547
r_dihedral_angle_4_deg25.502
r_dihedral_angle_3_deg12.459
r_dihedral_angle_1_deg6.225
r_angle_refined_deg1.684
r_angle_other_deg1.072
r_chiral_restr0.092
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.547
r_dihedral_angle_4_deg25.502
r_dihedral_angle_3_deg12.459
r_dihedral_angle_1_deg6.225
r_angle_refined_deg1.684
r_angle_other_deg1.072
r_chiral_restr0.092
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2548
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms44

Software

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