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Chimeric protein of human UFM1 E3 ligase, UFL1, and DDRGK1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Alphafold model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Sodium acetate trihydrate
Ammonium tartrate dibasic
Crystal Properties Matthews coefficient Solvent content 4.42 72.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.568 α = 90 b = 145.568 β = 90 c = 83.175 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 4M 2022-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.066 63.112 99.8 0.997 8.7 5.9 18967
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.066 3.28 0.446
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 Alphafold model 3.066 63.112 18956 936 99.716 0.235 0.2326 0.2326 0.2723 0.2722 123.573
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] -1.579 -0.789 -1.579 5.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.225 r_dihedral_angle_4_deg 23.791 r_lrange_it 16.847 r_scangle_it 14.93 r_dihedral_angle_3_deg 13.957 r_mcangle_it 11.77 r_scbond_it 10.824 r_mcbond_it 8.713 r_dihedral_angle_1_deg 6.158 r_angle_refined_deg 1.744
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.225 r_dihedral_angle_4_deg 23.791 r_lrange_it 16.847 r_scangle_it 14.93 r_dihedral_angle_3_deg 13.957 r_mcangle_it 11.77 r_scbond_it 10.824 r_mcbond_it 8.713 r_dihedral_angle_1_deg 6.158 r_angle_refined_deg 1.744 r_symmetry_nbd_refined 0.376 r_nbtor_refined 0.283 r_symmetry_xyhbond_nbd_refined 0.22 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.155 r_ncsr_local_group_1 0.1 r_chiral_restr 0.059 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4041 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing PARROT phasing Coot model building