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Crystal Structure of Human Fgr SH3-SH2-High Affinity Linker Mutant 2 (HAL2) 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 0.1 M trisodium citrate pH 5.5, 2.5 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.26 45.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.393 α = 90 b = 35.127 β = 100.642 c = 60.846 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 1.8 42.65 100 0.029 0.041 0.029 0.999 9.7 1.9 16998
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 1.8 1.84 100 0.621 0.879 0.621 0.485 1.1 2
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 1.8 42.65 16987 883 99.959 0.196 0.1944 0.1927 0.2331 0.2293 RANDOM 45.797
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] -1.24 -0.39 -1.105 2.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.516 r_dihedral_angle_6_deg 12.6 r_dihedral_angle_2_deg 9.063 r_dihedral_angle_1_deg 7.496 r_lrange_other 7.409 r_lrange_it 7.373 r_scangle_it 4.968 r_scangle_other 4.965 r_scbond_it 3.419 r_scbond_other 3.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.516 r_dihedral_angle_6_deg 12.6 r_dihedral_angle_2_deg 9.063 r_dihedral_angle_1_deg 7.496 r_lrange_other 7.409 r_lrange_it 7.373 r_scangle_it 4.968 r_scangle_other 4.965 r_scbond_it 3.419 r_scbond_other 3.417 r_mcangle_it 3.103 r_mcangle_other 3.102 r_mcbond_it 2.164 r_mcbond_other 2.151 r_angle_refined_deg 1.629 r_angle_other_deg 0.571 r_symmetry_nbd_refined 0.232 r_nbd_other 0.219 r_symmetry_nbd_other 0.201 r_nbd_refined 0.195 r_nbtor_refined 0.192 r_symmetry_xyhbond_nbd_refined 0.163 r_xyhbond_nbd_refined 0.116 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1251 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing Aimless data scaling xia2 data reduction