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Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole from cocktail screen)
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 2.73 55.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.48 α = 90 b = 35.558 β = 111.64 c = 58.11 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 2013-03-28 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 1.56 50 99.6 0.04 32.8 3.6 27496
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 1.56 1.59 94.3 0.193 5.1 2.9
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 1.56 50 26103 1382 99.49 0.17523 0.17428 0.1828 0.19314 0.2072 RANDOM 11.124
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] 0.92 0.36 -0.13 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.747 r_dihedral_angle_4_deg 14.761 r_dihedral_angle_3_deg 10.92 r_dihedral_angle_1_deg 5.483 r_scangle_it 3.585 r_scbond_it 2.156 r_mcangle_it 1.333 r_angle_refined_deg 1.308 r_angle_other_deg 0.833 r_mcbond_it 0.715
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.747 r_dihedral_angle_4_deg 14.761 r_dihedral_angle_3_deg 10.92 r_dihedral_angle_1_deg 5.483 r_scangle_it 3.585 r_scbond_it 2.156 r_mcangle_it 1.333 r_angle_refined_deg 1.308 r_angle_other_deg 0.833 r_mcbond_it 0.715 r_mcbond_other 0.159 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1241 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing