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INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z136583524
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 2.12 42.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.76 α = 90 b = 79.7 β = 90 c = 89.73 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 1.36 49.31 100 0.102 0.111 0.043 0.998 9.8 6.5 97220
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 1.36 1.4 99.9 1.698 1.866 0.766 0.406 5.9 7143
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 1.36 49.36 92302 4837 99.92 0.1791 0.1779 0.2019 0.2024 0.2211 RANDOM 17.812
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] -0.26 0.12 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.982 r_dihedral_angle_4_deg 21.919 r_dihedral_angle_3_deg 13.781 r_dihedral_angle_1_deg 7.004 r_mcangle_it 2.46 r_angle_refined_deg 1.607 r_angle_other_deg 1.442 r_mcbond_other 1.375 r_mcbond_it 1.366 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.982 r_dihedral_angle_4_deg 21.919 r_dihedral_angle_3_deg 13.781 r_dihedral_angle_1_deg 7.004 r_mcangle_it 2.46 r_angle_refined_deg 1.607 r_angle_other_deg 1.442 r_mcbond_other 1.375 r_mcbond_it 1.366 r_chiral_restr 0.084 r_bond_refined_d 0.009 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 445 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing