2B90

Crystal structure of the interleukin-4 variant T13DR85A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HIK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529452% Ammonium sulfate, 0.1M Sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.961.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.33α = 90
b = 91.33β = 90
c = 45.78γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IVRigaku VariMax mirror2004-08-19MSINGLE 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)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
12.145.799.40.05518.25.21180011729
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)
12.12.1898.70.2585.65.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1HIK2.120117801116255599.470.216090.216090.214450.24874RANDOM22.064
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]
0.630.63-1.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.044
r_scangle_it4.593
r_scbond_it2.788
r_mcangle_it1.715
r_angle_refined_deg1.661
r_mcbond_it0.87
r_symmetry_hbond_refined0.362
r_symmetry_vdw_refined0.344
r_xyhbond_nbd_refined0.274
r_nbd_refined0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.044
r_scangle_it4.593
r_scbond_it2.788
r_mcangle_it1.715
r_angle_refined_deg1.661
r_mcbond_it0.87
r_symmetry_hbond_refined0.362
r_symmetry_vdw_refined0.344
r_xyhbond_nbd_refined0.274
r_nbd_refined0.24
r_chiral_restr0.118
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1043
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing