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Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (2-fluoro-4-((4-phenylpiperidin-1-yl)sulfonyl)benzoyl)glycine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NFT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 2 M ammonium sulfate, 0.2 M sodium acetate, 0.1 M HEPES pH 7.5, 5% MPD
Crystal Properties Matthews coefficient Solvent content 2.87 57.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.575 α = 90 b = 53.575 β = 90 c = 54.097 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN A200 2020-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
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 1.55 38.1 99.3 0.044 0.047 0.016 0.998 33.5 7.8 22155
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 1.55 1.58 97.3 0.115 0.125 0.049 0.984 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 FOURIER SYNTHESIS THROUGHOUT 6NFT 1.55 38.07 21067 1075 99.27 0.1486 0.1478 0.1545 0.1638 0.1679 RANDOM 12.457
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] -0.22 -0.22 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.82 r_dihedral_angle_4_deg 20.786 r_dihedral_angle_3_deg 10.123 r_dihedral_angle_1_deg 6.572 r_angle_refined_deg 1.978 r_angle_other_deg 1.627 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.82 r_dihedral_angle_4_deg 20.786 r_dihedral_angle_3_deg 10.123 r_dihedral_angle_1_deg 6.572 r_angle_refined_deg 1.978 r_angle_other_deg 1.627 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 858 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 39
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction