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HHARI/ARIH1-UBCH7~Ubiquitin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 1 ul protein mixture with 10-12 mg/ml protein in 25 mM Tris pH 7.0, 150 mM NaCl, 1 mM DTT and 1 ul well solution with 7-10% PEG 5000 MME, 0.1 M HP pH 7.0 and 5% Tascimate pH 7.0. Over 1 ml reservoir.
Crystal Properties Matthews coefficient Solvent content 3.45 64.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.571 α = 90 b = 76.788 β = 107.33 c = 147.724 γ = 90
Symmetry Space Group C 1 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 PILATUS 6M-F double crystal Si(III) 2016-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.24 141.01 98.9 0.093 1 13.1 5.8 31387 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.24 3.45 96 0.883 0.76 1.9 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 3.24 141.01 29836 1550 98.92 0.22493 0.22211 0.2236 0.27906 0.2767 RANDOM 116.581
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] 3.56 -0.05 0.87 -3.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.625 r_dihedral_angle_4_deg 17.525 r_dihedral_angle_3_deg 16.673 r_long_range_B_refined 14.655 r_long_range_B_other 14.654 r_scangle_other 12.241 r_mcangle_it 10.768 r_mcangle_other 10.768 r_scbond_it 8.279 r_scbond_other 8.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.625 r_dihedral_angle_4_deg 17.525 r_dihedral_angle_3_deg 16.673 r_long_range_B_refined 14.655 r_long_range_B_other 14.654 r_scangle_other 12.241 r_mcangle_it 10.768 r_mcangle_other 10.768 r_scbond_it 8.279 r_scbond_other 8.279 r_mcbond_it 6.822 r_mcbond_other 6.821 r_dihedral_angle_1_deg 6.79 r_angle_refined_deg 1.382 r_angle_other_deg 1.019 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9166 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling CRANK phasing