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INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2856434821
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XY7 PDB entry 6XY7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 30 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 coefficient Solvent content 2.11 41.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.62 α = 90 b = 79.496 β = 90 c = 89.441 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 2019-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91589 Diamond I04-1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.58 62.65 100 0.152 0.166 0.066 0.982 8 6.3 61958
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) Redundancy Number Unique Reflections (All) 1 1.58 1.62 100 1.297 1.426 0.587 0.491 5.8 4530
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 6XY7 1.58 59.42 58770 3086 99.86 0.1843 0.1828 0.2076 0.213 0.2408 RANDOM 17.845
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 0.44 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.768 r_dihedral_angle_4_deg 24.978 r_dihedral_angle_3_deg 13.627 r_dihedral_angle_1_deg 7.113 r_mcangle_it 2.882 r_angle_refined_deg 1.519 r_mcbond_it 1.517 r_mcbond_other 1.51 r_angle_other_deg 1.353 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.768 r_dihedral_angle_4_deg 24.978 r_dihedral_angle_3_deg 13.627 r_dihedral_angle_1_deg 7.113 r_mcangle_it 2.882 r_angle_refined_deg 1.519 r_mcbond_it 1.517 r_mcbond_other 1.51 r_angle_other_deg 1.353 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3700 Nucleic Acid Atoms Solvent Atoms 437 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing