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The phosphatase and C2 domains of SHIP1 with covalent Z2738285202
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 41.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.674 α = 90 b = 79.378 β = 90 c = 89.573 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 79.4 100 0.998 8.5 13.2 88594
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 0.444
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 49.238 88485 2160 99.969 0.138 0.1371 0.1371 0.19 0.1903 19.476
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] -0.534 0.979 -0.445
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.595 r_dihedral_angle_4_deg 23.351 r_dihedral_angle_3_deg 12.458 r_dihedral_angle_other_3_deg 11.216 r_scbond_it 8.203 r_scbond_other 8.201 r_scangle_it 8.012 r_scangle_other 8.011 r_lrange_it 7.486 r_lrange_other 7.448
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.595 r_dihedral_angle_4_deg 23.351 r_dihedral_angle_3_deg 12.458 r_dihedral_angle_other_3_deg 11.216 r_scbond_it 8.203 r_scbond_other 8.201 r_scangle_it 8.012 r_scangle_other 8.011 r_lrange_it 7.486 r_lrange_other 7.448 r_dihedral_angle_1_deg 7.23 r_mcangle_it 3.982 r_mcangle_other 3.981 r_rigid_bond_restr 3.861 r_mcbond_other 3.143 r_mcbond_it 3.141 r_angle_refined_deg 1.785 r_angle_other_deg 1.457 r_nbd_refined 0.225 r_symmetry_nbd_other 0.189 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.17 r_symmetry_nbd_refined 0.154 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.062 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_xyhbond_nbd_other 0.006 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 527 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing