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The Crystal Structure of SHP1 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HJP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Hepes pH7.5, 2% PEG 400, 2.0M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.14 42.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.302 α = 90 b = 56.498 β = 90 c = 110.258 γ = 90
Symmetry Space Group P 21 2 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 EIGER X 9M 2023-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95373 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 45.3 99.9 0.088 16.4 13.4 29341
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 0.975
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 1.75 39.488 29270 1420 99.836 0.194 0.1925 0.2014 0.2266 0.2333 30.129
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] -1.927 1.386 0.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.518 r_dihedral_angle_3_deg 10.294 r_dihedral_angle_1_deg 6.321 r_lrange_it 5.234 r_lrange_other 5.183 r_dihedral_angle_2_deg 4.274 r_scangle_it 3.539 r_scangle_other 3.538 r_mcangle_it 2.583 r_mcangle_other 2.582
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.518 r_dihedral_angle_3_deg 10.294 r_dihedral_angle_1_deg 6.321 r_lrange_it 5.234 r_lrange_other 5.183 r_dihedral_angle_2_deg 4.274 r_scangle_it 3.539 r_scangle_other 3.538 r_mcangle_it 2.583 r_mcangle_other 2.582 r_scbond_it 2.137 r_scbond_other 2.137 r_mcbond_it 1.587 r_mcbond_other 1.586 r_angle_refined_deg 1.087 r_angle_other_deg 0.404 r_nbd_refined 0.2 r_symmetry_nbd_other 0.181 r_nbd_other 0.178 r_nbtor_refined 0.174 r_symmetry_nbd_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.127 r_xyhbond_nbd_refined 0.121 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.058 r_symmetry_xyhbond_nbd_other 0.027 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2254 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing