8R0J

Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl guanylhydrazone, 2a

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	293	18% PEG 3350, 150 mM NaK tartrate, pH 7.4;

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.15	α = 90
b = 130.34	β = 90
c = 146.89	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 EIGER X 9M		2021-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87313	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.4	48.746	99.9	0.398	0.992	6.5	12.8		37129

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	2.4	2.45			0.506	1.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.4	48.746	37065	1855	99.938	0.189	0.1853	0.2498	44.962

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]
0.777			0.273		-1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.739
r_dihedral_angle_6_deg	14.04
r_lrange_it	8.648
r_lrange_other	8.584
r_dihedral_angle_2_deg	7.832
r_scangle_it	6.071
r_scangle_other	6.071
r_dihedral_angle_1_deg	5.415
r_mcangle_it	4.675
r_mcangle_other	4.675
r_scbond_it	3.655
r_scbond_other	3.655
r_mcbond_it	2.888
r_mcbond_other	2.888
r_angle_refined_deg	1.409
r_angle_other_deg	0.524
r_nbd_other	0.259
r_symmetry_xyhbond_nbd_refined	0.259
r_nbd_refined	0.215
r_symmetry_nbd_other	0.202
r_symmetry_nbd_refined	0.201
r_xyhbond_nbd_refined	0.196
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_other	0.115
r_ncsr_local_group_2	0.115
r_ncsr_local_group_1	0.11
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.074
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_xyhbond_nbd_other	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7514
Nucleic Acid Atoms
Solvent Atoms	417
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing