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The phosphatase and C2 domains of SHIP1 with covalent Z56948267
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 sulphate, 100 mM MES/imidazole 20 % PEG 500 MME, 10% PEG 20,000
Crystal Properties Matthews coefficient Solvent content 2.11 41.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.711 α = 90 b = 79.568 β = 90 c = 89.631 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 EIGER2 XE 16M 2021-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.4 51.4 100 0.998 9.6 12 88912
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 100 0.422 1.1 12
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.4 49.301 88830 1964 99.984 0.134 0.1326 0.1326 0.1898 0.19 21.222
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] 0.032 0.661 -0.693
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.944 r_dihedral_angle_4_deg 21.016 r_dihedral_angle_3_deg 12.952 r_dihedral_angle_1_deg 7.418 r_lrange_it 6.272 r_lrange_other 6.147 r_scbond_it 5.659 r_scbond_other 5.658 r_scangle_it 5.409 r_scangle_other 5.408
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.944 r_dihedral_angle_4_deg 21.016 r_dihedral_angle_3_deg 12.952 r_dihedral_angle_1_deg 7.418 r_lrange_it 6.272 r_lrange_other 6.147 r_scbond_it 5.659 r_scbond_other 5.658 r_scangle_it 5.409 r_scangle_other 5.408 r_mcangle_it 5.135 r_mcangle_other 5.134 r_mcbond_it 3.901 r_mcbond_other 3.89 r_rigid_bond_restr 3.105 r_angle_refined_deg 1.77 r_angle_other_deg 1.463 r_nbd_other 0.225 r_nbd_refined 0.22 r_symmetry_xyhbond_nbd_other 0.199 r_symmetry_nbd_refined 0.192 r_symmetry_nbd_other 0.19 r_symmetry_xyhbond_nbd_refined 0.187 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.171 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3721 Nucleic Acid Atoms Solvent Atoms 493 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing