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INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2737076969
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 41.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.668 α = 90 b = 79.429 β = 90 c = 89.54 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 2019-08-03 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 1.22 79.44 99.8 0.108 0.118 0.047 0.997 6.9 5.9 132919
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 1.22 1.25 98.1 1.074 1.233 0.593 0.45 4.1 9560
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 1.22 59.42 126180 6637 99.68 0.181 0.1799 0.2018 0.201 0.225 RANDOM 14.849
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] -0.36 0.24 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.423 r_dihedral_angle_4_deg 23.857 r_dihedral_angle_3_deg 13.382 r_dihedral_angle_1_deg 7.223 r_mcangle_it 2.111 r_angle_refined_deg 1.645 r_angle_other_deg 1.442 r_mcbond_other 1.146 r_mcbond_it 1.14 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.423 r_dihedral_angle_4_deg 23.857 r_dihedral_angle_3_deg 13.382 r_dihedral_angle_1_deg 7.223 r_mcangle_it 2.111 r_angle_refined_deg 1.645 r_angle_other_deg 1.442 r_mcbond_other 1.146 r_mcbond_it 1.14 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3700 Nucleic Acid Atoms Solvent Atoms 454 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing