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Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U9B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294 0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 2.71 54.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.237 α = 90 b = 35.492 β = 111.82 c = 58.122 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 93 CCD MARMOSAIC 300 mm CCD 2013-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 1.14 50 94.4 0.046 30.8 3.4 65740
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 1.14 1.16 67.5 0.269 3 2.6
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 1U9B 1.14 50 62405 3311 94.39 0.1567 0.15559 0.162 0.17777 0.1845 RANDOM 10.817
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] -0.4 -0.64 -0.41 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.315 r_dihedral_angle_4_deg 17.231 r_dihedral_angle_3_deg 10.301 r_scangle_it 5.805 r_dihedral_angle_1_deg 5.69 r_scbond_it 3.885 r_mcangle_it 2.88 r_angle_refined_deg 1.941 r_mcbond_it 1.865 r_rigid_bond_restr 1.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.315 r_dihedral_angle_4_deg 17.231 r_dihedral_angle_3_deg 10.301 r_scangle_it 5.805 r_dihedral_angle_1_deg 5.69 r_scbond_it 3.885 r_mcangle_it 2.88 r_angle_refined_deg 1.941 r_mcbond_it 1.865 r_rigid_bond_restr 1.569 r_angle_other_deg 0.946 r_mcbond_other 0.536 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.007 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1241 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing