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UCHL3 in complex with synthetic, K27-linked diubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ 1UBQ, 1UCH experimental model PDB 1UCH 1UBQ, 1UCH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298.15 Drops set up in MRC 2 well, 96 well plate using a Mosquito crystallization robot. 100+100 nl drops.
Best crystals:
21% PEG 3350
0.15M KBr
0.1M Bis-Tris pH 5.5
Crystals grow also in KCl and AmSO4 (0.2 M), or with PEG 200 MME. Crystals can be obtained at 4C as well.
Crystal Properties Matthews coefficient Solvent content 2.67 54.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.29 α = 90 b = 81.206 β = 90 c = 159.858 γ = 90
Symmetry Space Group P 2 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 2M 2017-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 79.929 99.9 0.092 0.115 0.046 9.8 6.4 54231
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 100 0.99 0.99 0.049 0.019 0.7 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1UBQ, 1UCH 2.1 44.3 51455 2684 99.79 0.1866 0.1843 0.195 0.2332 0.2403 RANDOM 55.422
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] -1.62 0.5 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.918 r_dihedral_angle_4_deg 18.833 r_dihedral_angle_3_deg 15.317 r_dihedral_angle_1_deg 6.594 r_angle_refined_deg 1.486 r_angle_other_deg 1.231 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.918 r_dihedral_angle_4_deg 18.833 r_dihedral_angle_3_deg 15.317 r_dihedral_angle_1_deg 6.594 r_angle_refined_deg 1.486 r_angle_other_deg 1.231 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6044 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing