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CRYSTAL STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME FROM NAEGLERIA FOWLERI, APO FORM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 MORPHEUS E9 (50 MM TRIS-HCL, 50 MM
BICINE PH 8.5, 30 MM DIETHYLENE GLYCOL; 30 MM TRIETHYLENE GLYCOL;
30 MM TETRAETHYLENE GLYCOL; 30 MM PETAETHYLENE GLYCOL; 20%
GLYCEROL; 10% PEG 4000, TRAY 303865 PUCK RBT2-03, VAPOR
DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 1.86 33.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.3 α = 90 b = 42.87 β = 90 c = 89.96 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 RIGAKU SATURN 944+ 2018-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 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 1.85 50 99.9 0.045 30.4 9.76 12875 -3 31.29
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 1.85 1.9 99.9 0.589 2.94 5516
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5V0R 1.85 38.7 1.35 12875 1311 99.9 0.187 0.183 0.1829 0.222 0.2223 28.55
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1116 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement XDS data reduction PHASER phasing