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Crystal structure of K27-linked di-ubiquitin in complex with synthetic antigen binding fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KEO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 290 0.005 M cobalt(II) chloride hexahydrate, 0.005 M Nickel(II) chloride hexahydrate, 0.005 M Cadmium chloride hydrate, 0.005 M Magnesium chloride hexahydrate ,0.1 M HEPES pH 7.5, 12% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.4 48.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.34 α = 90 b = 71.5 β = 95.08 c = 93.91 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 PILATUS3 6M 2019-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03321 APS 23-ID-D
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 2.2 68.7 99.2 0.998 9.75 3.8 61619
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 2.2 2.26 98.9 0.685 3.9
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 THROUGHOUT 2.2 68.69 1.35 61619 3084 99.13 0.2004 0.1987 0.201 0.2326 0.2348
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 12.73 f_angle_d 0.525 f_chiral_restr 0.042 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8979 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing