5XEJ

Crystal Structure of Macrophage Migration Inhibitory Factor bound to MTX


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GDG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.1M HEPES(pH7.5), 65% Sat. AS, 2% PEG400
Crystal Properties
Matthews coefficientSolvent content
3.7266.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.758α = 90
b = 95.758β = 90
c = 104.154γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102006-09-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32B21.0SPring-8BL32B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.51001000.0968.48.919607
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.591000.3399.2

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 REPLACEMENTTHROUGHOUT2GDG2.583.051858299899.980.18290.18050.2272RANDOM20.926
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]
-0.2-0.1-0.20.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.117
r_dihedral_angle_4_deg22.008
r_dihedral_angle_3_deg13.944
r_dihedral_angle_1_deg6.053
r_angle_refined_deg2.023
r_angle_other_deg1.058
r_chiral_restr0.105
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.117
r_dihedral_angle_4_deg22.008
r_dihedral_angle_3_deg13.944
r_dihedral_angle_1_deg6.053
r_angle_refined_deg2.023
r_angle_other_deg1.058
r_chiral_restr0.105
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2601
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms53

Software

Software
Software NamePurpose
HKL-2000data processing
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKLdata reduction
HKLdata scaling