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Crystal structure of Plasmodium falciparum ubiquitin conjugating enzyme UBC9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other search model found using BALBES software
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2 M NaF, 20% PEG3350 Cryo: 30% PEG3350, 10% glycerol, 0.2M NaF, 100mM glycine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 46.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.87 α = 90 b = 94.39 β = 90.02 c = 124.89 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 ADSC QUANTUM 315 2010-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9795 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 25 93.59 53373 53373 2 0.5
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 Balbes automatic selection 1.851 24.978 1.37 53373 53373 2867 93.59 0.1491 0.1462 0.1487 0.1883 0.1851
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 13.227 f_angle_d 1.599 f_chiral_restr 0.053 f_plane_restr 0.01 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5111 Nucleic Acid Atoms Solvent Atoms 1137 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection MOLREP phasing BALBES phasing PHENIX refinement XDS data reduction XSCALE data scaling