2AZ5 | pdb_00002az5

Crystal Structure of TNF-alpha with a small molecule inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TNF	PDB Entry: 1TNF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	2.5 M Sodium Formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 165.254	α = 90
b = 165.254	β = 90
c = 63.728	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		IMAGE PLATE	MARRESEARCH		2003-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.0	SSRL	BL7-1

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	2.1	20					37559

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 (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	PDB Entry: 1TNF	2.1	20	37535	1916	99.2	0.227	0.227	0.22	0.2167	0.278	0.2784	RANDOM	36.784

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]
-0.57	-0.29		-0.57		0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.195
r_dihedral_angle_4_deg	15.132
r_dihedral_angle_3_deg	14.902
r_dihedral_angle_1_deg	6.734
r_scangle_it	5.359
r_mcangle_it	4.87
r_scbond_it	3.598
r_mcbond_it	3.42
r_angle_refined_deg	1.396
r_nbtor_refined	0.311
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.185
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.091
r_symmetry_hbond_refined	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4194
Nucleic Acid Atoms
Solvent Atoms	226
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing