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Crystal structure of the SMA homodimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1M HEPES buffer pH 7.0, 1M Succinic acid and 1% w/v PEG2000 MME
Crystal Properties Matthews coefficient Solvent content 2.19 43.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.816 α = 90 b = 56.816 β = 90 c = 59.78 γ = 120
Symmetry Space Group P 31 1 2
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 2022-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
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 2.13 49.2 98.5 0.107 0.094 0.994 5 3.4 6216 33.24
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 2.13 2.19 82.1 0.835 0.768 0.6 1 3.2
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 THROUGHOUT 2.15 28.424 6154 311 99.805 0.194 0.1903 0.1928 0.2538 0.2563 RANDOM 37.882
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] -1.139 -0.57 -1.139 3.695
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.739 r_dihedral_angle_6_deg 13.079 r_lrange_it 7.412 r_lrange_other 7.368 r_dihedral_angle_1_deg 7.334 r_scangle_it 6.121 r_scangle_other 6.116 r_mcangle_it 4.622 r_mcangle_other 4.619 r_dihedral_angle_2_deg 4.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.739 r_dihedral_angle_6_deg 13.079 r_lrange_it 7.412 r_lrange_other 7.368 r_dihedral_angle_1_deg 7.334 r_scangle_it 6.121 r_scangle_other 6.116 r_mcangle_it 4.622 r_mcangle_other 4.619 r_dihedral_angle_2_deg 4.533 r_scbond_it 4.045 r_scbond_other 4.041 r_mcbond_it 3.402 r_mcbond_other 3.368 r_angle_refined_deg 1.725 r_angle_other_deg 0.576 r_symmetry_xyhbond_nbd_refined 0.239 r_symmetry_nbd_other 0.207 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.195 r_nbtor_refined 0.176 r_symmetry_nbd_refined 0.16 r_nbd_other 0.141 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.08 r_bond_refined_d 0.007 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 898 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing