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PanDDA analysis - Crystal structure of the Ubiquitin conjugating enzyme 4 from Leishmania major (LmUbC4) in complex with Z111782404
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 28HT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 3.1 M NaCl, 0.1 M MES/imid pH 6.5, 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.73 54.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.109 α = 90 b = 116.109 β = 90 c = 154.197 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 9M 2024-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.921344 Diamond I04-1
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 2.329 84.28 100 1 14.3 20.6 17350 81.71
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 2.329 2.37 99.4 0.42 0.3
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 2.329 84.23 16990 849 97.9 0.2533 0.251 0.2351 0.296 0.2872 RANDOM 109.83
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] 12.0176 12.0176 -24.0352
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.24 t_omega_torsion 2.75 t_angle_deg 0.88 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.24 t_omega_torsion 2.75 t_angle_deg 0.88 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2576 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 32
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling DIMPLE phasing