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Crystal structure of chimeric UFC1, TAK MotiF replaced with HPN motif of other E2 proteins
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.1M sodium citrate tribasic dihydrate pH 5.5, 20% w/v 2-propanol, 20% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.163 α = 90 b = 47.163 β = 90 c = 144.632 γ = 90
Symmetry Space Group P 41 21 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 9M 2025-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.543 44.84 99.86 0.03874 0.999 12.8 2 24971 20.41
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.543 1.598 98.65 0.9574 0.525 0.81 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.543 44.839 24971 1259 99.868 0.191 0.1902 0.2023 0.2088 0.2236 21.516
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] -0.067 -0.067 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.57 r_dihedral_angle_4_deg 19.497 r_dihedral_angle_3_deg 11.5 r_dihedral_angle_1_deg 6.564 r_lrange_it 6.25 r_lrange_other 6.177 r_scangle_it 5.138 r_scangle_other 5.135 r_scbond_it 3.454 r_scbond_other 3.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.57 r_dihedral_angle_4_deg 19.497 r_dihedral_angle_3_deg 11.5 r_dihedral_angle_1_deg 6.564 r_lrange_it 6.25 r_lrange_other 6.177 r_scangle_it 5.138 r_scangle_other 5.135 r_scbond_it 3.454 r_scbond_other 3.452 r_mcangle_it 2.866 r_mcangle_other 2.864 r_mcbond_it 1.914 r_mcbond_other 1.914 r_angle_refined_deg 1.583 r_angle_other_deg 1.431 r_symmetry_nbd_refined 0.243 r_nbd_refined 0.213 r_symmetry_nbd_other 0.19 r_nbd_other 0.182 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.133 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1362 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling Coot model building