4CNM | pdb_00004cnm

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	PDB	3ZYJ	PDB ENTRY 3ZYJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				THE CRYSTALLIZATION DROP CONTAINED 100 NL OF CONCENTRATED 5T4 (5.5 MG/ML), 100 NL OF 25% W/V POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M CITRATE PH 3.5, AND 0.5 NL OF 0.1 M NAOH

Crystal Properties
Matthews coefficient	Solvent content
1.9	34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.31	α = 90
b = 67.31	β = 90
c = 96.38	γ = 90

Symmetry
Space Group	P 21 21 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	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	1.75	49.31	99.8	0.07	17.9	9.6		33062		3.1

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	1.75	1.8	99.2		0.81	3.1	9.3

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 (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 3ZYJ	1.75	43.94	31330	1674	99.76	0.18365	0.18172	0.19	0.22153	0.23	RANDOM	35.524

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]
-1.32			3.22		-1.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.2
r_dihedral_angle_4_deg	18.166
r_dihedral_angle_3_deg	12.762
r_dihedral_angle_1_deg	6.43
r_scbond_it	3.656
r_mcangle_it	2.814
r_mcbond_it	1.943
r_mcbond_other	1.942
r_angle_refined_deg	1.833
r_angle_other_deg	0.929
r_chiral_restr	0.109
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.002
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	2201
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	130

Software

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