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Crystal structure of the UBA domain of Dsk2 in complex with Ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ PDB ENTRIES 1UBQ AND 2BWB experimental model PDB 2BWB PDB ENTRIES 1UBQ AND 2BWB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.2M MAGNESIUM CHLORIDE, 0.1M TRIS PH 8.5, 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.19 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.971 α = 90 b = 77.972 β = 90 c = 49.485 γ = 120
Symmetry Space Group P 31 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 DYNAMICALLY BENDABLE MIRROR 2011-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.52 67.5 99.5 0.05 27.78 8.07 27296 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.62 98.1 0.37 4.55 7.93
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 PDB ENTRIES 1UBQ AND 2BWB 1.51 67.52 27090 1359 99.22 0.15921 0.15722 0.164 0.19615 0.1973 RANDOM 20.21
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] -0.28 -0.14 -0.28 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.837 r_sphericity_free 30.19 r_sphericity_bonded 19.09 r_dihedral_angle_4_deg 18.616 r_dihedral_angle_3_deg 14.686 r_rigid_bond_restr 6.477 r_dihedral_angle_1_deg 5.904 r_angle_refined_deg 2.087 r_angle_other_deg 1.097 r_chiral_restr 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.837 r_sphericity_free 30.19 r_sphericity_bonded 19.09 r_dihedral_angle_4_deg 18.616 r_dihedral_angle_3_deg 14.686 r_rigid_bond_restr 6.477 r_dihedral_angle_1_deg 5.904 r_angle_refined_deg 2.087 r_angle_other_deg 1.097 r_chiral_restr 0.16 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d 0.003 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 893 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SADABS data scaling PHASER phasing