7KP8 | pdb_00007kp8

asymmetric mTNF-alpha hTNFR1 complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		unpublished structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.65	298	800 mM sodium potassium tartrate, 0.45% PEG 5000 MME, 100 mM Tris, pH7.65. Vapor diffusion, sitting drop, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.89	68.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.577	α = 90
b = 133.577	β = 90
c = 141.445	γ = 90

Symmetry
Space Group	P 41 21 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	MARMOSAIC 225 mm CCD		2012-08-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.9787	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	3.15	50	99.9	0.19	0.188	0.212	0.095	8.3	4.9		22757

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.15	3.32	100		0.896	0.896	1.007	0.45	0.8	5

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X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	unpublished structure	3.15	48.61	22704	1152	99.85	0.2241	0.2216	0.221	0.2716	0.2629	RANDOM	67.3777

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]
1.78			1.78		-3.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.092
r_dihedral_angle_4_deg	18.605
r_dihedral_angle_3_deg	16.12
r_dihedral_angle_1_deg	7.305
r_angle_refined_deg	1.222
r_angle_other_deg	0.937
r_chiral_restr	0.068
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4903
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	33

Software

Software
Software Name	Purpose
XDS	data reduction
SCALA	data scaling
REFMAC	refinement
PHASER	phasing