5UZY

Crystal structure of N97A 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
2.7254.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.134α = 90
b = 68.269β = 90
c = 86.392γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2017-01-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
11.715099.70.0660.0720.0288.14.744201
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)
11.711.7499.40.1990.240.1320.9463

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 REPLACEMENTTHROUGHOUT3DJH1.7148.2341899216699.420.15670.15560.1785RANDOM14.798
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]
0.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.01
r_dihedral_angle_4_deg19.618
r_dihedral_angle_3_deg11.261
r_dihedral_angle_1_deg5.453
r_angle_other_deg4.879
r_angle_refined_deg2.023
r_chiral_restr0.144
r_bond_refined_d0.026
r_gen_planes_other0.021
r_gen_planes_refined0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.01
r_dihedral_angle_4_deg19.618
r_dihedral_angle_3_deg11.261
r_dihedral_angle_1_deg5.453
r_angle_other_deg4.879
r_angle_refined_deg2.023
r_chiral_restr0.144
r_bond_refined_d0.026
r_gen_planes_other0.021
r_gen_planes_refined0.011
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2558
Nucleic Acid Atoms
Solvent Atoms312
Heterogen Atoms38

Software

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