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The phosphatase and C2 domains of SHIP1 with covalent Z1742148362
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 2.09 41.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.508 α = 90 b = 79.171 β = 90 c = 89.378 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 1.45 79.2 100 0.998 8 12.9 79287
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 1.45 1.47 100 0.453
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 1.45 51.276 79176 2097 99.95 0.146 0.144 0.1531 0.2018 0.1984 20.658
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] -0.088 0.478 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.157 r_dihedral_angle_4_deg 22.961 r_dihedral_angle_3_deg 12.713 r_dihedral_angle_other_3_deg 8.335 r_dihedral_angle_1_deg 7.375 r_lrange_it 6.017 r_lrange_other 5.866 r_scangle_it 5.543 r_scangle_other 5.542 r_mcangle_it 4.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.157 r_dihedral_angle_4_deg 22.961 r_dihedral_angle_3_deg 12.713 r_dihedral_angle_other_3_deg 8.335 r_dihedral_angle_1_deg 7.375 r_lrange_it 6.017 r_lrange_other 5.866 r_scangle_it 5.543 r_scangle_other 5.542 r_mcangle_it 4.903 r_mcangle_other 4.902 r_scbond_it 4.36 r_scbond_other 4.359 r_mcbond_it 3.841 r_mcbond_other 3.84 r_rigid_bond_restr 3.089 r_angle_refined_deg 1.753 r_angle_other_deg 1.455 r_nbd_refined 0.238 r_nbd_other 0.228 r_symmetry_nbd_refined 0.213 r_symmetry_xyhbond_nbd_refined 0.211 r_symmetry_nbd_other 0.195 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_other 0.102 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3704 Nucleic Acid Atoms Solvent Atoms 482 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing