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Ube2D1 in complex with ubiquitin variant Ubv.D1.1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PTF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 24% PEG2000-MME, 0.2M trimethylamine N-oxide, 0.1M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.55 51.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.12 α = 90 b = 52.565 β = 90 c = 96.748 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 100 CCD ADSC QUANTUM 315 2014-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.1 50 99.9 0.104 0.112 0.047 30.2 7.2 15572 41.91
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 99.6 1 1 0.573 0.61 1.46 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3PTF 2.11 48.37 1.34 15521 787 99.6 0.2151 0.2142 0.231 0.2274 56.99
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.3878 f_angle_d 0.5988 f_chiral_restr 0.0442 f_plane_restr 0.0034 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1726 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement DENZO data reduction HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction