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Structure of UbV.d2.1 in complex with Ube2d2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TGD experimental model PDB 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 289 0.1 M Sodium citrate pH 5.6,
20% w/v PEG 4000,
20% v/v 2-Propanol
Crystal Properties Matthews coefficient Solvent content 2.9 57.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.774 α = 90 b = 129.774 β = 90 c = 123.106 γ = 120
Symmetry Space Group P 31 2 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 16M 2020-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 2.99 44.66 99.8 0.181 0.188 0.051 0.999 14.4 13.5 24533
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 2.99 3.18 99 1.699 1.765 0.475 0.703 13.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.99 41.5 1.34 24497 1145 99.83 0.2492 0.2469 0.2466 0.2954 0.2963
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.19 f_angle_d 0.553 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6499 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing