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Crystal structure of the Ubiquitin Conjugating Enzyme 4 from Leishmania major (LmUbC4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 3 M NaCl, 0.1 M MES/imidazole pH 6.5, 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.51 51.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115 α = 90 b = 115 β = 90 c = 151.542 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 PILATUS 6M 2023-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.99990 ELETTRA 11.2C
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 2.157 83.23 95.9 0.998 20.1 18.9 20142
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 2.157 2.194 100 0.357 0.9
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 2.16 83.23 19106 939 95.88 0.19243 0.19114 0.2043 0.22424 0.2398 RANDOM 72.612
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] 0.31 0.15 0.31 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.235 r_long_range_B_refined 8.347 r_long_range_B_other 8.346 r_dihedral_angle_2_deg 6.288 r_scangle_other 6.285 r_dihedral_angle_1_deg 6.039 r_mcangle_other 4.658 r_mcangle_it 4.652 r_scbond_it 3.855 r_scbond_other 3.854
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.235 r_long_range_B_refined 8.347 r_long_range_B_other 8.346 r_dihedral_angle_2_deg 6.288 r_scangle_other 6.285 r_dihedral_angle_1_deg 6.039 r_mcangle_other 4.658 r_mcangle_it 4.652 r_scbond_it 3.855 r_scbond_other 3.854 r_mcbond_it 3.059 r_mcbond_other 3.026 r_angle_refined_deg 1.295 r_angle_other_deg 0.486 r_chiral_restr 0.07 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 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 2583 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing