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Crystal Structure of Shank2-SAM domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F44
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 0.1M Bis Tris pH5.5, 0.3M of Magnesium formate
Crystal Properties Matthews coefficient Solvent content 2.82 56.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.49 α = 90 b = 57.49 β = 90 c = 48.033 γ = 120
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 16M 2021-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9762 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 49.8 99.92 0.2587 0.05916 0.996 10.07 19.8 5201
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 100 1.42 0.3268 0.568 1.61 19.7
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 2F44 2.117 49.788 5122 247 98.085 0.198 0.1956 0.1951 0.2517 0.2504 38.747
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] 0.269 0.135 0.269 -0.873
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.586 r_dihedral_angle_4_deg 22.922 r_dihedral_angle_3_deg 14.627 r_lrange_it 7.996 r_lrange_other 7.996 r_dihedral_angle_1_deg 5.684 r_scangle_other 5.497 r_scangle_it 5.495 r_mcangle_it 3.774 r_mcangle_other 3.769
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.586 r_dihedral_angle_4_deg 22.922 r_dihedral_angle_3_deg 14.627 r_lrange_it 7.996 r_lrange_other 7.996 r_dihedral_angle_1_deg 5.684 r_scangle_other 5.497 r_scangle_it 5.495 r_mcangle_it 3.774 r_mcangle_other 3.769 r_scbond_it 3.546 r_scbond_other 3.521 r_mcbond_it 2.641 r_mcbond_other 2.64 r_angle_refined_deg 1.488 r_angle_other_deg 1.22 r_xyhbond_nbd_refined 0.249 r_metal_ion_refined 0.249 r_symmetry_nbd_refined 0.248 r_nbd_refined 0.214 r_symmetry_nbd_other 0.177 r_symmetry_xyhbond_nbd_refined 0.164 r_nbtor_refined 0.15 r_nbd_other 0.125 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_other 0.075 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 570 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing