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Crystal structure of the SMA:VH1 Complex at 1.2 A resolution
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, HANGING DROP 5.5 293 Bis-Tris buffer at pH 5.5 and 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.03 39.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.813 α = 90 b = 53.544 β = 90 c = 99.07 γ = 90
Symmetry Space Group P 21 21 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 EIGER2 XE 16M 2023-07-29 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 1.2 49.54 97.8 0.036 0.022 0.999 22.1 6.2 63942 9.04
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 79.7 0.167 0.127 4.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.2 47.149 63861 3214 97.638 0.113 0.1118 0.1437 0.1441 RANDOM 11.043
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] 0.291 0.041 -0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.899 r_lrange_it 12.546 r_lrange_other 10.803 r_dihedral_angle_3_deg 10.397 r_dihedral_angle_2_deg 9.307 r_dihedral_angle_1_deg 7.109 r_scangle_it 6.937 r_scangle_other 6.934 r_mcangle_other 5.068 r_mcangle_it 5.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.899 r_lrange_it 12.546 r_lrange_other 10.803 r_dihedral_angle_3_deg 10.397 r_dihedral_angle_2_deg 9.307 r_dihedral_angle_1_deg 7.109 r_scangle_it 6.937 r_scangle_other 6.934 r_mcangle_other 5.068 r_mcangle_it 5.067 r_scbond_it 5.012 r_scbond_other 5.01 r_rigid_bond_restr 4.221 r_mcbond_it 3.519 r_mcbond_other 3.514 r_angle_refined_deg 1.976 r_angle_other_deg 0.725 r_xyhbond_nbd_other 0.321 r_symmetry_xyhbond_nbd_refined 0.317 r_symmetry_nbd_refined 0.29 r_nbd_refined 0.254 r_xyhbond_nbd_refined 0.25 r_symmetry_nbd_other 0.206 r_nbd_other 0.203 r_nbtor_refined 0.179 r_chiral_restr 0.11 r_symmetry_nbtor_other 0.09 r_symmetry_xyhbond_nbd_other 0.02 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1779 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing