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UbcH5c~Ubiquitin Conjugate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TGD PDB ENTRIES 3TGD AND 1UBQ experimental model PDB 1UBQ PDB ENTRIES 3TGD AND 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.2M tri-potassium citrate, 20% PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.28 45.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.027 α = 90 b = 52.51 β = 101.07 c = 53.114 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 113 CCD RIGAKU SATURN 944+ mirrors 2011-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.35 52.51 97.1 0.048 19.2 4.89 9319 9319
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 2.35 2.43 78.2 0.204 5 3.11
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRIES 3TGD AND 1UBQ 2.35 29.618 1.37 9298 9298 467 96.95 0.213 0.2108 0.2004 0.2524 0.2431
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] -3.8773 3.1039 3.4703 0.407
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.97 f_angle_d 1.071 f_chiral_restr 0.089 f_bond_d 0.014 f_plane_restr 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1767 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 12
Software Software Software Name Purpose StructureStudio data collection PHENIX model building PHENIX refinement d*TREK data reduction d*TREK data scaling PHENIX phasing