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The phosphatase and C2 domains of SHIP1 with covalent Z1763271112
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 41.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.498 α = 90 b = 78.993 β = 90 c = 89.289 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) R Merge I (Observed) 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 1.3 62.5 100 0.096 0.04 1 11.6 12.7 109198
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 100 0.998 0.581 0.7 12.3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.3 59.163 109094 2038 99.983 0.147 0.146 0.1905 0.1809 19.077
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] -0.198 0.299 -0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.066 r_dihedral_angle_3_deg 13.41 r_dihedral_angle_2_deg 12.829 r_dihedral_angle_1_deg 7.283 r_rigid_bond_restr 4.64 r_lrange_it 4.137 r_lrange_other 3.84 r_scangle_it 2.963 r_scangle_other 2.963 r_dihedral_angle_other_3_deg 2.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.066 r_dihedral_angle_3_deg 13.41 r_dihedral_angle_2_deg 12.829 r_dihedral_angle_1_deg 7.283 r_rigid_bond_restr 4.64 r_lrange_it 4.137 r_lrange_other 3.84 r_scangle_it 2.963 r_scangle_other 2.963 r_dihedral_angle_other_3_deg 2.826 r_mcangle_it 2.568 r_mcangle_other 2.568 r_scbond_it 2.106 r_scbond_other 2.105 r_mcbond_it 1.887 r_mcbond_other 1.883 r_angle_refined_deg 1.779 r_angle_other_deg 0.626 r_dihedral_angle_other_2_deg 0.32 r_symmetry_nbd_refined 0.217 r_symmetry_xyhbond_nbd_other 0.206 r_nbd_refined 0.201 r_symmetry_nbd_other 0.196 r_nbd_other 0.187 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.17 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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 532 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing