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Human SHIP1 with magnesium and phosphate bound to the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OKM
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, pH 6.5, 20 % PEG 500 MME, 10% PEG 20,000
Crystal Properties Matthews coefficient Solvent content 2.09 41.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.5 α = 90 b = 79.088 β = 90 c = 89.255 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 2019-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.8266 Diamond I03
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 1.086 59.193 87.6 0.152 0.155 0.03 0.998 11.7 26.9 159826
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 1.093 1.14 59.6 2.19 2.246 0.48 0.601 1.4 20.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5OKM 1.086 59.193 159810 1775 85.905 0.136 0.1358 0.1358 0.1587 0.1586 14.339
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] 0.079 -0.008 -0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.754 r_dihedral_angle_4_deg 25.458 r_dihedral_angle_3_deg 12.711 r_dihedral_angle_1_deg 7.442 r_lrange_it 3.416 r_lrange_other 3.283 r_scangle_it 2.709 r_scangle_other 2.708 r_mcangle_other 2.483 r_mcangle_it 2.481
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.754 r_dihedral_angle_4_deg 25.458 r_dihedral_angle_3_deg 12.711 r_dihedral_angle_1_deg 7.442 r_lrange_it 3.416 r_lrange_other 3.283 r_scangle_it 2.709 r_scangle_other 2.708 r_mcangle_other 2.483 r_mcangle_it 2.481 r_scbond_it 2.127 r_scbond_other 2.127 r_rigid_bond_restr 1.901 r_mcbond_it 1.889 r_mcbond_other 1.881 r_angle_refined_deg 1.702 r_angle_other_deg 1.465 r_symmetry_nbd_refined 0.223 r_nbd_other 0.222 r_nbd_refined 0.213 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.165 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3704 Nucleic Acid Atoms Solvent Atoms 489 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DIALS data reduction STARANISO data scaling PHASER phasing