8R02 | pdb_00008r02

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2R17

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	293	20% PEG 3350, 150 mM NaK tartrate, 100 mM NaCl, pH 7.4

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.5	α = 90
b = 140.83	β = 90
c = 141.34	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-F		2021-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91788	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.5	19.919	99.7	0.999	16.1	13.6		40494

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	2.5	2.55			0.597

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.5	19.919	40436	2021	99.729	0.205	0.2017	0.2	0.2639	0.27	115.59

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]
5.565			-3.074		-2.491

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.753
r_dihedral_angle_3_deg	17.184
r_dihedral_angle_6_deg	13.914
r_lrange_it	13.71
r_lrange_other	13.71
r_scangle_it	10.748
r_scangle_other	10.747
r_mcangle_it	9.957
r_mcangle_other	9.956
r_scbond_it	7.041
r_scbond_other	7.041
r_mcbond_it	6.839
r_mcbond_other	6.839
r_dihedral_angle_1_deg	5.848
r_angle_refined_deg	1.444
r_angle_other_deg	0.804
r_nbd_other	0.336
r_nbd_refined	0.224
r_symmetry_nbd_other	0.215
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.177
r_xyhbond_nbd_refined	0.14
r_ncsr_local_group_2	0.113
r_symmetry_xyhbond_nbd_refined	0.103
r_ncsr_local_group_1	0.097
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.074
r_symmetry_xyhbond_nbd_other	0.025
r_bond_refined_d	0.008
r_gen_planes_other	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7729
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	18

Software

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