3L9J

Selection of a novel highly specific TNFalpha antagonist: Insight from the crystal structure of the antagonist-TNFalpha complex

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TNF	PDB ENTRY 1TNF for chain T and 1TN3 for chain C; For 1TN3 the randomized loops was removed from teh search model. These loop is 116-122 (loop 1) and 145-150 (loop 4)
experimental model	PDB	1TN3	PDB ENTRY 1TNF for chain T and 1TN3 for chain C; For 1TN3 the randomized loops was removed from teh search model. These loop is 116-122 (loop 1) and 145-150 (loop 4)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.1M Tris, 0.35M MgAc, 20% 2-propanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.905	α = 90
b = 83.905	β = 90
c = 149.172	γ = 120

Symmetry
Space Group	P 63 2 2

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	MARRESEARCH			M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.81500	EMBL/DESY, HAMBURG	X12
2	SYNCHROTRON	MAX II BEAMLINE I911-3	1.0	MAX II	I911-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	74	99.86			17880	17855	3	3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1TNF for chain T and 1TN3 for chain C; For 1TN3 the randomized loops was removed from teh search model. These loop is 116-122 (loop 1) and 145-150 (loop 4)	2.1	41.95	17855	968	99.86	0.175	0.173	0.217	RANDOM	29.367

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]
0.29	0.15		0.29		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.431
r_dihedral_angle_4_deg	18.222
r_dihedral_angle_3_deg	13.126
r_dihedral_angle_1_deg	6.42
r_scangle_it	4.718
r_scbond_it	2.915
r_mcangle_it	1.977
r_angle_refined_deg	1.475
r_mcbond_it	1.129
r_symmetry_hbond_refined	0.319
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.234
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.191
r_chiral_restr	0.11
r_metal_ion_refined	0.045
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2206
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing