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Crystal structure of human UBA6 in complex with the ubiquitin-like modifier FAT10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PVN 7PVN, 6GF1, 6GF2 experimental model PDB 6GF1 7PVN, 6GF1, 6GF2 experimental model PDB 6GF2 7PVN, 6GF1, 6GF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 277 0.5 M Lithium chloride, 0.1 M Tris pH 8.4, 25% PEG 6000
Crystal Properties Matthews coefficient Solvent content 3.56 65.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.458 α = 70.519 b = 93.593 β = 88.537 c = 109.542 γ = 74.593
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 2021-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9677 ESRF ID30B
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 3.268 46.093 59.07 0.202 0.236 0.12 0.9881 5.2 3.84 30812 90.24
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 3.268 3.705 53.4 1.092 1.266 0.64 0.401 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 7PVN, 6GF1, 6GF2 3.27 45.14 1.96 30793 875 59.03 0.2166 0.2159 0.2184 0.2392 0.2431 111.34
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 17.3229 f_angle_d 0.7573 f_chiral_restr 0.0439 f_plane_restr 0.0076 f_bond_d 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16503 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing