7ZA2

GPC3-Unc5D octamer structure and role in cell migration

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	291.15	15% w/v PEG 3000, 20% v/v 1, 2, 4-butanetrol, 1% w/v NDSB 256, 0.1 M Gly-GLy/AMPD (pH 8.5) and 0.2 M of amino acids (DL-arginine HCL, DL-threonine, DL-histidine HCL H2O, DL-5-hydroxylysine HCL, trans-4-hydroxyl-L-proline).

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.113	α = 90
b = 157.994	β = 102.91
c = 126.572	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 EIGER2 XE 16M		2018-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97950	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	4.6	66.62	99.7	0.09281	0.03962	0.997	7.77	6.6		21870			245.99

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	4.6	4.76			0.485	1.81

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-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5FTT, GPC3	4.6	66.616	21812	1866	99.621	0.311	0.3075	0.347	331.565

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]
15.254		9.105	-7.738		-10.578

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.361
r_lrange_it	34.816
r_lrange_other	34.816
r_dihedral_angle_3_deg	17.498
r_mcangle_it	16.75
r_mcangle_other	16.749
r_scangle_it	15.207
r_scangle_other	15.207
r_dihedral_angle_4_deg	13.212
r_mcbond_it	9.703
r_mcbond_other	9.701
r_scbond_it	8.308
r_scbond_other	8.307
r_dihedral_angle_1_deg	3.74
r_angle_other_deg	1.521
r_angle_refined_deg	1.384
r_symmetry_nbd_refined	0.325
r_nbd_other	0.312
r_nbd_refined	0.228
r_symmetry_nbd_other	0.209
r_xyhbond_nbd_refined	0.2
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_other	0.138
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19188
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	257

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing