5EIZ

Crystal structure of Y99A 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
2.754.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.696α = 90
b = 67.958β = 90
c = 86.519γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2015-04-30MSINGLE 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
11.965099.10.0390.0450.02124.64.228977
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)
11.961.9994.80.0590.070.0360.9933.31367

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 3DJH1.9647.9627443148698.980.15790.15660.1811RANDOM17.733
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_deg42.7
r_dihedral_angle_4_deg20.212
r_dihedral_angle_3_deg11.026
r_dihedral_angle_1_deg4.994
r_angle_other_deg3.757
r_angle_refined_deg1.82
r_mcangle_it1.777
r_mcbond_it1.366
r_mcbond_other1.358
r_chiral_restr0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.7
r_dihedral_angle_4_deg20.212
r_dihedral_angle_3_deg11.026
r_dihedral_angle_1_deg4.994
r_angle_other_deg3.757
r_angle_refined_deg1.82
r_mcangle_it1.777
r_mcbond_it1.366
r_mcbond_other1.358
r_chiral_restr0.122
r_bond_refined_d0.022
r_gen_planes_other0.02
r_gen_planes_refined0.011
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2530
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms41

Software

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