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INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z26548083
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 2.06 40.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.25 α = 90 b = 78.73 β = 90 c = 89.07 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 2019-10-24 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 1.65 51.02 99.6 0.164 0.178 0.069 0.997 7.9 6.6 53143
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 1.65 1.69 98.9 2.445 2.642 0.993 0.34 6.9 3817
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 1.65 51.08 50424 2662 99.46 0.1778 0.176 0.2037 0.2134 0.24 RANDOM 21.44
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] -0.97 1.27 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.767 r_dihedral_angle_4_deg 22.16 r_dihedral_angle_3_deg 14.149 r_dihedral_angle_1_deg 6.899 r_mcangle_it 2.447 r_angle_refined_deg 1.447 r_mcbond_other 1.33 r_mcbond_it 1.324 r_angle_other_deg 1.32 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.767 r_dihedral_angle_4_deg 22.16 r_dihedral_angle_3_deg 14.149 r_dihedral_angle_1_deg 6.899 r_mcangle_it 2.447 r_angle_refined_deg 1.447 r_mcbond_other 1.33 r_mcbond_it 1.324 r_angle_other_deg 1.32 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 435 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing