3NFP | pdb_00003nfp

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)
Type	Source	Accession Code	Details
experimental model	PDB	3NFS	PDB ENTRY 3NFS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.1 M Tris-HCl, 0.2M MgCl2, 10% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.167	α = 90
b = 114.973	β = 90
c = 247.555	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX225HE		2009-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9796	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.8	50	95.5	0.158	7.1	4.6		31671

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	99.8		0.384	2.9	3.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3NFS	2.86	50	31669	1599	93.08	0.255	0.253	0.25	0.301	0.25	RANDOM	69.528

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			-2.44		1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.654
r_dihedral_angle_3_deg	15.662
r_dihedral_angle_4_deg	13.085
r_mcangle_it	4.92
r_dihedral_angle_1_deg	4.889
r_scangle_it	4.827
r_rigid_bond_restr	4.542
r_scbond_it	3.902
r_mcbond_it	3.146
r_sphericity_bonded	1.559

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.654
r_dihedral_angle_3_deg	15.662
r_dihedral_angle_4_deg	13.085
r_mcangle_it	4.92
r_dihedral_angle_1_deg	4.889
r_scangle_it	4.827
r_rigid_bond_restr	4.542
r_scbond_it	3.902
r_mcbond_it	3.146
r_sphericity_bonded	1.559
r_sphericity_free	1.457
r_angle_refined_deg	1.052
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8324
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.