5MIX

Extracellular domain of human CD83 - trigonal crystal form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.4 microliter protein (39 mg/ml in 50 mM Tris-HCl (pH 8.0) buffer) were mixed with 0.2 microliter reservoir solution (1 M ammonium sulfate, 0.1 M HEPES (pH 7.0), 0.5% w/v polyethylene glycol (PEG) 8000) and equilibrated against 70 microliter of reservoir solution
Crystal Properties
Matthews coefficientSolvent content
1.7931.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.942α = 90
b = 62.942β = 90
c = 40.064γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918409BESSY14.1

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
11.740.0699.90.04623.89.91034838.5
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)
11.71.899.90.8512.69.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFREE R-VALUE1.70140.061.3810347102699.920.19120.18840.216444.6
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
f_dihedral_angle_d12.682
f_angle_d1.088
f_chiral_restr0.049
f_bond_d0.006
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms597
Nucleic Acid Atoms
Solvent Atoms31
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
XDSdata reduction
Cootmodel building