7ZA1

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	20% ethylene glycol, 10% w/v PEG 8000, 0.1 M Tris/BICINE (pH 8.5) and 0.02 M of amino acids (L-Na-glutamate, alanine, glycine, lysine-HCl, and serine)

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.643	α = 90
b = 157.584	β = 102.949
c = 126.601	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-F		2018-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	4.1	123.4	73	0.109	0.13	0.071	0.994	3.4	3.4		22459			143.4

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	4.1	4.55	10.9		0.738	1.6	3.5

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5FTT, hGPC3	4.1	97.336	18399	899	59.546	0.326	0.3239	0.3648	186.258

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]
0.883		1.725	3.2		-4.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.776
r_lrange_it	17.238
r_lrange_other	17.238
r_dihedral_angle_3_deg	16.034
r_dihedral_angle_4_deg	12.084
r_mcangle_it	6.562
r_mcangle_other	6.562
r_scangle_it	5.457
r_scangle_other	5.457
r_mcbond_it	3.643
r_mcbond_other	3.642
r_dihedral_angle_1_deg	3.233
r_scbond_it	2.882
r_scbond_other	2.882
r_angle_refined_deg	1.572
r_angle_other_deg	1.556
r_symmetry_nbd_refined	0.345
r_nbd_other	0.309
r_nbd_refined	0.235
r_xyhbond_nbd_refined	0.228
r_symmetry_nbd_other	0.214
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.108
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.032
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19184
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	462

Software

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