5RY3

INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2027158783


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
2.0840.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.432α = 90
b = 79.136β = 90
c = 89.221γ = 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
11.559.21000.2060.2240.0880.9936.26.471958
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)
11.51.581001.8422.0320.850.4195.710390

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 6XY71.559.267922355299.380.18410.18290.2077RANDOM16.516
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]
-0.330.59-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.26
r_dihedral_angle_4_deg23.33
r_dihedral_angle_3_deg13.742
r_dihedral_angle_1_deg7.12
r_mcangle_it2.319
r_angle_refined_deg1.529
r_angle_other_deg1.385
r_mcbond_it1.243
r_mcbond_other1.243
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.26
r_dihedral_angle_4_deg23.33
r_dihedral_angle_3_deg13.742
r_dihedral_angle_1_deg7.12
r_mcangle_it2.319
r_angle_refined_deg1.529
r_angle_other_deg1.385
r_mcbond_it1.243
r_mcbond_other1.243
r_chiral_restr0.079
r_bond_refined_d0.008
r_gen_planes_refined0.008
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 Atoms443
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing