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Crystal Structure of Human Fgr SH3-SH2-High Affinity Linker Mutant 3 (HAL3) Domains.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7UY0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298.15 0.2 M sodium chloride, 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 46.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.613 α = 90 b = 34.907 β = 101.519 c = 61.315 γ = 90
Symmetry Space Group P 1 21 1
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 X CdTe 16M kb bent focusing mirror 2021-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0 APS 23-ID-D
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 1.6 60.08 99.7 0.13 0.136 0.038 0.999 13.9 12.3 24665
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 1.6 1.63 95.9 2.126 2.261 0.749 0.7 2.3 8.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 60.08 24654 1219 99.652 0.17 0.1691 0.1686 0.1935 0.1947 RANDOM 21.687
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] -0.015 -0.806 -0.844 1.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.387 r_dihedral_angle_3_deg 12.319 r_dihedral_angle_2_deg 8.013 r_dihedral_angle_1_deg 7.65 r_lrange_it 6.385 r_lrange_other 6.356 r_scangle_it 4.003 r_scangle_other 4.001 r_scbond_it 2.685 r_scbond_other 2.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.387 r_dihedral_angle_3_deg 12.319 r_dihedral_angle_2_deg 8.013 r_dihedral_angle_1_deg 7.65 r_lrange_it 6.385 r_lrange_other 6.356 r_scangle_it 4.003 r_scangle_other 4.001 r_scbond_it 2.685 r_scbond_other 2.684 r_mcangle_it 1.977 r_mcangle_other 1.976 r_angle_refined_deg 1.966 r_mcbond_it 1.301 r_mcbond_other 1.3 r_angle_other_deg 0.804 r_symmetry_nbd_refined 0.216 r_nbd_refined 0.206 r_nbtor_refined 0.183 r_symmetry_nbd_other 0.169 r_nbd_other 0.156 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.134 r_chiral_restr 0.107 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_other 0.061 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1313 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Coot model building PHASER phasing Aimless data scaling xia2 data reduction