3NFP

Crystal structure of the Fab fragment of therapeutic antibody daclizumab in complex with IL-2Ra (CD25) ectodomain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NFSPDB ENTRY 3NFS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.1 M Tris-HCl, 0.2M MgCl2, 10% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5451.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.167α = 90
b = 114.973β = 90
c = 247.555γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2009-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9796SSRFBL17U

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
12.85095.50.1587.14.631671
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)
12.82.999.80.3842.93.9

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 3NFS2.865031669159993.080.2550.2530.301RANDOM69.528
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]
1.41-2.441.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.654
r_dihedral_angle_3_deg15.662
r_dihedral_angle_4_deg13.085
r_mcangle_it4.92
r_dihedral_angle_1_deg4.889
r_scangle_it4.827
r_rigid_bond_restr4.542
r_scbond_it3.902
r_mcbond_it3.146
r_sphericity_bonded1.559
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.654
r_dihedral_angle_3_deg15.662
r_dihedral_angle_4_deg13.085
r_mcangle_it4.92
r_dihedral_angle_1_deg4.889
r_scangle_it4.827
r_rigid_bond_restr4.542
r_scbond_it3.902
r_mcbond_it3.146
r_sphericity_bonded1.559
r_sphericity_free1.457
r_angle_refined_deg1.052
r_chiral_restr0.067
r_bond_refined_d0.007
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8324
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms

Software

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