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X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ 1UBQ, 1X23 experimental model PDB 1X23 1UBQ, 1X23
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM
TCEP) at 20 mg/ml with 1.5 ul of reservoir solution (0.1 M Tris pH 8.5 and 24% PEG 10,000), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.16 43.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.462 α = 90 b = 102.903 β = 90 c = 159.806 γ = 90
Symmetry Space Group P 21 21 21
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 325 mm CCD 2006-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97918 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.7 50 97.4 0.128 17.4 5.3 13165 13156 -3 59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 98.3 0.458 3.2 5.3 1309
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1UBQ, 1X23 2.7 50 13247 13133 622 97.52 0.21177 0.21177 0.2087 0.27538 0.2442 RANDOM 43.342
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] 0.97 -1.82 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.352 r_dihedral_angle_3_deg 15.719 r_dihedral_angle_4_deg 13.739 r_scangle_it 5.951 r_dihedral_angle_1_deg 5.649 r_mcangle_it 4.661 r_scbond_it 3.513 r_mcbond_it 2.619 r_angle_refined_deg 1.095 r_angle_other_deg 0.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.352 r_dihedral_angle_3_deg 15.719 r_dihedral_angle_4_deg 13.739 r_scangle_it 5.951 r_dihedral_angle_1_deg 5.649 r_mcangle_it 4.661 r_scbond_it 3.513 r_mcbond_it 2.619 r_angle_refined_deg 1.095 r_angle_other_deg 0.808 r_mcbond_other 0.505 r_chiral_restr 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3600 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling