7A17 | pdb_00007a17

Crystal structure of the 5-phosphatase domain of Synaptojanin1 bound to its substrate diC8-PI(3,4,5)P3 in complex with a nanobody

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I9Y	1i9y, 3n9v, 3mtc, 4cmn, 4nc2
experimental model	PDB	3N9V	1i9y, 3n9v, 3mtc, 4cmn, 4nc2
experimental model	PDB	3MTC	1i9y, 3n9v, 3mtc, 4cmn, 4nc2
experimental model	PDB	4CMN	1i9y, 3n9v, 3mtc, 4cmn, 4nc2
experimental model	PDB	4NC2	1i9y, 3n9v, 3mtc, 4cmn, 4nc2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	15% PEG 3350, 0.1 M sodium citrate pH 5.5, 13% ethanol

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 169.323	α = 90
b = 109.205	β = 120.62
c = 100.902	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER X 9M		2019-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.976246	SOLEIL	PROXIMA 2

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	2.728	87.39	91.5	0.2	0.282	0.148	0.97	5.3	3.5		32151			43.28

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	2.728	3.02			0.474	1.4	3.6

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1i9y, 3n9v, 3mtc, 4cmn, 4nc2	2.73	87.39	30520	1630	76.22	0.19881	0.19578	0.2	0.25744	0.26	RANDOM	43.603

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]
0.45		-0.41	0.37		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.129
r_dihedral_angle_4_deg	16.634
r_dihedral_angle_3_deg	15.703
r_long_range_B_refined	8.871
r_long_range_B_other	8.871
r_mcangle_it	6.054
r_mcangle_other	6.054
r_scangle_other	5.789
r_dihedral_angle_1_deg	5.754
r_mcbond_it	3.752
r_mcbond_other	3.751
r_scbond_it	3.632
r_scbond_other	3.632
r_angle_refined_deg	1.079
r_angle_other_deg	0.934
r_chiral_restr	0.066
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10616
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	85

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building