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

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1I9Y1i9y, 3n9v, 3mtc, 4cmn, 4nc2
experimental modelPDB 3N9V1i9y, 3n9v, 3mtc, 4cmn, 4nc2
experimental modelPDB 3MTC1i9y, 3n9v, 3mtc, 4cmn, 4nc2
experimental modelPDB 4CMN1i9y, 3n9v, 3mtc, 4cmn, 4nc2
experimental modelPDB 4NC21i9y, 3n9v, 3mtc, 4cmn, 4nc2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529315% PEG 3350, 0.1 M sodium citrate pH 5.5, 13% ethanol
Crystal Properties
Matthews coefficientSolvent content
2.4249.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.323α = 90
b = 109.205β = 120.62
c = 100.902γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2019-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.976246SOLEILPROXIMA 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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.72887.3991.50.20.2820.1480.975.33.53215143.28
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.7283.020.4741.43.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1i9y, 3n9v, 3mtc, 4cmn, 4nc22.7387.3930520163076.220.198810.195780.20.257440.26RANDOM43.603
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]
0.45-0.410.37-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.129
r_dihedral_angle_4_deg16.634
r_dihedral_angle_3_deg15.703
r_long_range_B_refined8.871
r_long_range_B_other8.871
r_mcangle_it6.054
r_mcangle_other6.054
r_scangle_other5.789
r_dihedral_angle_1_deg5.754
r_mcbond_it3.752
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.129
r_dihedral_angle_4_deg16.634
r_dihedral_angle_3_deg15.703
r_long_range_B_refined8.871
r_long_range_B_other8.871
r_mcangle_it6.054
r_mcangle_other6.054
r_scangle_other5.789
r_dihedral_angle_1_deg5.754
r_mcbond_it3.752
r_mcbond_other3.751
r_scbond_it3.632
r_scbond_other3.632
r_angle_refined_deg1.079
r_angle_other_deg0.934
r_chiral_restr0.066
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms10616
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms85

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building