7ZA3

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	7.8	291.15	0.1M Tris (pH 7.8) 5% w/v gamma-PGA, 20% w/vPEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.577	α = 90
b = 119.577	β = 90
c = 257.936	γ = 120

Symmetry
Space Group	P 31

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		2017-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.80000	Diamond	I03

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	80.878	73.8	0.053	0.02	1	12.6	8.2		26038			269.6

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	4.227			0.761	2

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	80.878	26038	1333	74.8	0.357	0.3553	0.3846	301.314

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]
2.071	1.036		2.071		-6.719

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.398
r_lrange_it	39.988
r_lrange_other	39.988
r_mcangle_it	18.852
r_mcangle_other	18.852
r_dihedral_angle_3_deg	17.758
r_scangle_it	15.027
r_scangle_other	15.026
r_dihedral_angle_4_deg	13.208
r_mcbond_other	10.807
r_mcbond_it	10.806
r_scbond_it	8.141
r_scbond_other	8.141
r_dihedral_angle_1_deg	3.907
r_angle_other_deg	1.485
r_angle_refined_deg	1.375
r_symmetry_nbd_refined	0.715
r_nbd_other	0.559
r_symmetry_xyhbond_nbd_refined	0.508
r_xyhbond_nbd_other	0.324
r_nbd_refined	0.23
r_symmetry_nbd_other	0.209
r_xyhbond_nbd_refined	0.202
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_other	0.163
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.067
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
autoPROC	data reduction
xia2	data scaling
PHENIX	phasing