5RXP

INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2856434944


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529330 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Crystal Properties
Matthews coefficientSolvent content
2.141.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.49α = 90
b = 79.39β = 90
c = 89.34γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91589DiamondI04-1

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
11.5379.391000.1120.1230.0490.99810.1667742
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.531.5799.91.1831.3490.640.4864.34924

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 6XY71.5359.3464323334899.910.17520.17390.2018RANDOM17.868
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]
-0.720.91-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.504
r_dihedral_angle_4_deg23.557
r_dihedral_angle_3_deg13.779
r_dihedral_angle_1_deg7.187
r_mcangle_it2.543
r_angle_refined_deg1.582
r_angle_other_deg1.42
r_mcbond_it1.372
r_mcbond_other1.369
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.504
r_dihedral_angle_4_deg23.557
r_dihedral_angle_3_deg13.779
r_dihedral_angle_1_deg7.187
r_mcangle_it2.543
r_angle_refined_deg1.582
r_angle_other_deg1.42
r_mcbond_it1.372
r_mcbond_other1.369
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3700
Nucleic Acid Atoms
Solvent Atoms438
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing