4CNC | pdb_00004cnc

Crystal structure of human 5T4 (Wnt-activated inhibitory factor 1, Trophoblast glycoprotein)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		5T4, CRYSTAL FORM WITH 1 MOLECULE IN THE ASYMMETRIC UNIT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP			THE CRYSTALLIZATION SITTING DROP CONTAINED 100 NL OF CONCENTRATED 5T4/WAIF1 (5 MG/ML IN 20 MM TRIS-HCL, PH 7.5, 150 MM NACL) PLUS 100 NL OF 0.2 M (NH4)2SO4, 30 % W/V PEG 4000.

Crystal Properties
Matthews coefficient	Solvent content
1.8	33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.6	α = 90
b = 95.82	β = 91.14
c = 65.97	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M	KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING	2013-04-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

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	1.77	54.33	99.7	0.06	13.8	5		59830		2.5

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	1.77	1.82	99.5		0.76	2.5	4.9

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	5T4, CRYSTAL FORM WITH 1 MOLECULE IN THE ASYMMETRIC UNIT	1.77	54.33	56784	3022	99.72	0.17929	0.17725	0.19	0.21727	0.22	RANDOM	32.234

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]
-1.1		0.03	-0.77		1.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.632
r_dihedral_angle_4_deg	17.533
r_dihedral_angle_3_deg	12.937
r_dihedral_angle_1_deg	6.314
r_scbond_it	3.597
r_mcangle_it	2.694
r_angle_refined_deg	1.905
r_mcbond_it	1.838
r_mcbond_other	1.829
r_angle_other_deg	0.917
r_chiral_restr	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4268
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	257

Software

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