5BSJ

Crystal structure of S63A mutant of human macrophage migration inhibitory factor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DJHPDB entry 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
3.7266.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.785α = 90
b = 95.785β = 90
c = 103.889γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2015-05-21MSINGLE 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
125099.80.0520.0570.02317.55.837683
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)
122.0398.80.090.10.0440.9915.11813

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 REPLACEMENTTHROUGHOUTPDB entry 3DJH247.8935797181299.650.18450.18320.2105RANDOM22.824
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.689
r_dihedral_angle_4_deg22.754
r_dihedral_angle_3_deg11.423
r_dihedral_angle_1_deg4.718
r_angle_other_deg4.306
r_mcangle_it2.59
r_mcbond_it2.153
r_mcbond_other2.153
r_angle_refined_deg1.854
r_chiral_restr0.128
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.689
r_dihedral_angle_4_deg22.754
r_dihedral_angle_3_deg11.423
r_dihedral_angle_1_deg4.718
r_angle_other_deg4.306
r_mcangle_it2.59
r_mcbond_it2.153
r_mcbond_other2.153
r_angle_refined_deg1.854
r_chiral_restr0.128
r_bond_refined_d0.023
r_gen_planes_other0.019
r_gen_planes_refined0.01
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2525
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms46

Software

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