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Crystal structure of UBE2J2 in complex with ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F4W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293.15 18% V/V 2-Propanol, 100mM sodium acetate trihydrate, 20% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.34 47.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.879 α = 90 b = 46.201 β = 98.2 c = 55.239 γ = 90
Symmetry Space Group P 1 21 1
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 2024-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.967697 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.32 52.34 98.9 0.126 0.143 0.067 0.993 10.5 4.5 11468
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.4 99.5 0.661 0.748 0.343 0.621 4.7
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 (Observed) 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 2.32 52.34 10855 601 98.61 0.19359 0.19047 0.2012 0.24729 0.2513 RANDOM 34.774
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] -0.37 -0.82 0.44 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.542 r_dihedral_angle_2_deg 11.452 r_long_range_B_refined 9.582 r_long_range_B_other 9.58 r_scangle_other 7.357 r_dihedral_angle_1_deg 6.896 r_mcangle_other 4.708 r_mcangle_it 4.706 r_scbond_it 4.66 r_scbond_other 4.659
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.542 r_dihedral_angle_2_deg 11.452 r_long_range_B_refined 9.582 r_long_range_B_other 9.58 r_scangle_other 7.357 r_dihedral_angle_1_deg 6.896 r_mcangle_other 4.708 r_mcangle_it 4.706 r_scbond_it 4.66 r_scbond_other 4.659 r_mcbond_it 3.188 r_mcbond_other 3.156 r_angle_refined_deg 1.826 r_angle_other_deg 0.576 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1925 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction