1M48 | pdb_00001m48

Crystal Structure of Human IL-2 Complexed with (R)-N-[2-[1-(Aminoiminomethyl)-3-piperidinyl]-1-oxoethyl]-4-(phenylethynyl)-L-phenylalanine methyl ester

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.47	α = 90
b = 58.02	β = 90
c = 93.08	γ = 90

Symmetry
Space Group	P 21 21 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	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2000-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.95	10	98.1	0.059	0.059	11.4	2.65	20214	20214			23.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.95	2.016	94.3		0.357	0.357	3.1	2.4	1846

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.95	10	19081	19081	974	98.41	0.20046	0.20046	0.19716	0.2	0.26891	0.27	RANDOM	33.028

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]
0.84			0.71		-1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	5.354
r_mcangle_it	5.027
r_scbond_it	3.744
r_mcbond_it	3.259
r_dihedral_angle_1_deg	2.778
r_angle_refined_deg	1.422
r_symmetry_vdw_refined	0.341
r_symmetry_hbond_refined	0.286
r_nbd_refined	0.22
r_chiral_restr	0.121

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	5.354
r_mcangle_it	5.027
r_scbond_it	3.744
r_mcbond_it	3.259
r_dihedral_angle_1_deg	2.778
r_angle_refined_deg	1.422
r_symmetry_vdw_refined	0.341
r_symmetry_hbond_refined	0.286
r_nbd_refined	0.22
r_chiral_restr	0.121
r_xyhbond_nbd_refined	0.112
r_bond_refined_d	0.008
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2025
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	66

Software

Software
Software Name	Purpose
d*TREK	data reduction
AMoRE	phasing
REFMAC	refinement
d*TREK	data scaling

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.