4GAF | pdb_00004gaf

Crystal structure of EBI-005, a chimera of human IL-1beta and IL-1Ra, bound to human Interleukin-1 receptor type 1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	20% PEG 3350, 100 mM Tris, 200 mM lithium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.35	α = 90
b = 149.27	β = 90
c = 126.17	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 MX-300		2011-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9755	CLSI	08ID-1

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	2.15	50	99.9	0.061	12.8	5.6	175866	31476	1	1

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	2.15	2.23	100		0.56		5.6	3102

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.15	41.86	31383	1585	100	0.2183	0.2155	0.2215	0.2712	0.2809	RANDOM	53.367

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]
0.18			-0.59		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.358
r_dihedral_angle_4_deg	22.557
r_dihedral_angle_3_deg	18.993
r_dihedral_angle_1_deg	7.479
r_scangle_it	5.356
r_scbond_it	3.324
r_mcangle_it	2.209
r_angle_refined_deg	1.983
r_mcbond_it	1.232
r_chiral_restr	0.145

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.358
r_dihedral_angle_4_deg	22.557
r_dihedral_angle_3_deg	18.993
r_dihedral_angle_1_deg	7.479
r_scangle_it	5.356
r_scbond_it	3.324
r_mcangle_it	2.209
r_angle_refined_deg	1.983
r_mcbond_it	1.232
r_chiral_restr	0.145
r_bond_refined_d	0.022
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3716
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	57

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.