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The 1.1A crystallographic structure of ubiquitin-conjugating enzyme (ubc-2) from Caenorhabditis elegans: functional and evolutionary significance
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QCQ pdb entry 1qcq
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 capillary counter-diffusion 5 277.5 7mg/mL protein in 2mM sodium citrate, 10% (v/v) ethanol, 1.5M Sodium Chloride, pH 5.0, capillary counter-diffusion, temperature 277.5K
Crystal Properties Matthews coefficient Solvent content 2.2 44.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.604 α = 90 b = 60.457 β = 106.45 c = 43.98 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 CCD MAR CCD 165 mm 2002-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97 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 1.1 30 97.4 0.055 5.5 58674
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 1.14 92.6 0.143 3 5541
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 (All) 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 entry 1qcq 1.1 30 57952 5900 96.162 0.132 0.1305 0.1404 0.1493 0.1575 RANDOM 7.614
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] 0.264 -0.109 0.037 -0.362
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.045 r_dihedral_angle_1_deg 14.377 r_dihedral_angle_4_deg 13.566 r_dihedral_angle_3_deg 12.506 r_sphericity_free 6.899 r_scangle_it 3.151 r_sphericity_bonded 2.914 r_mcangle_it 2.548 r_scbond_it 2.292 r_mcbond_it 1.724
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.045 r_dihedral_angle_1_deg 14.377 r_dihedral_angle_4_deg 13.566 r_dihedral_angle_3_deg 12.506 r_sphericity_free 6.899 r_scangle_it 3.151 r_sphericity_bonded 2.914 r_mcangle_it 2.548 r_scbond_it 2.292 r_mcbond_it 1.724 r_scangle_other 1.639 r_mcangle_other 1.588 r_angle_refined_deg 1.335 r_rigid_bond_restr 1.206 r_scbond_other 1.041 r_angle_other_deg 0.889 r_mcbond_other 0.873 r_symmetry_vdw_refined 0.386 r_symmetry_vdw_other 0.221 r_nbd_refined 0.216 r_nbtor_refined 0.188 r_nbd_other 0.184 r_xyhbond_nbd_refined 0.111 r_metal_ion_refined 0.111 r_chiral_restr 0.086 r_nbtor_other 0.086 r_symmetry_hbond_refined 0.047 r_symmetry_metal_ion_refined 0.024 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1175 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement CNS refinement SCALEPACK data scaling MAR345 data collection CNS phasing