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Crystal structure of K33 linked di-Ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 100mM sodium acetate, 200mM lithium sulphate, 50% PEG400
Crystal Properties Matthews coefficient Solvent content 1.66 25.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.48 α = 90 b = 57.017 β = 95.45 c = 33.984 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 PILATUS 6M-F 2014-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.999 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.65 33.83 99.4 0.1033 10.55 4.3 13474 12779
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 99.04 4.4
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 1.65 33.83 12779 693 99.38 0.16493 0.16235 0.1757 0.21353 0.2186 RANDOM 12.587
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] 0.24 -0.69 0.11 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.581 r_dihedral_angle_4_deg 20.334 r_dihedral_angle_3_deg 13.142 r_dihedral_angle_1_deg 7.242 r_long_range_B_other 4.403 r_long_range_B_refined 4.402 r_scangle_other 3.278 r_scbond_it 2.172 r_scbond_other 2.165 r_angle_refined_deg 1.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.581 r_dihedral_angle_4_deg 20.334 r_dihedral_angle_3_deg 13.142 r_dihedral_angle_1_deg 7.242 r_long_range_B_other 4.403 r_long_range_B_refined 4.402 r_scangle_other 3.278 r_scbond_it 2.172 r_scbond_other 2.165 r_angle_refined_deg 1.986 r_mcangle_other 1.472 r_mcangle_it 1.471 r_mcbond_it 1.026 r_mcbond_other 1.012 r_angle_other_deg 0.913 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1182 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 22
Software Software Software Name Purpose XDS data reduction SCALA data scaling REFMAC refinement PHASER phasing