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Toxoplasma gondii ubiquitin conjugating enzyme TgTwinScan_2721- E2 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.4 297 32% Peg 1500, 0.2 M MgCl2, 0.1 M Tris pH
8.4, 10 mM Spermidine, VAPOR DIFFUSION, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.36 47.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.475 α = 90 b = 141.334 β = 90 c = 77.13 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE RIGAKU RAXIS IV VeriMax 2005-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.12 50 98.8 0.077 0.077 7.6 6.3 23386 23386 36.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.16 97.3 0.729 0.729 2.22 6.3 1143
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) 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 2BEP 2.11 50 22605 22605 763 98.66 0.19992 0.19992 0.1987 0.2009 0.23779 0.1998 RANDOM 35.401
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] 1.22 -0.73 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.176 r_dihedral_angle_4_deg 27.115 r_dihedral_angle_3_deg 16.543 r_dihedral_angle_1_deg 6.386 r_scangle_it 4.977 r_scbond_it 3.206 r_mcangle_it 2.137 r_angle_refined_deg 1.892 r_mcbond_it 1.339 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.176 r_dihedral_angle_4_deg 27.115 r_dihedral_angle_3_deg 16.543 r_dihedral_angle_1_deg 6.386 r_scangle_it 4.977 r_scbond_it 3.206 r_mcangle_it 2.137 r_angle_refined_deg 1.892 r_mcbond_it 1.339 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.271 r_xyhbond_nbd_refined 0.255 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.15 r_chiral_restr 0.129 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2259 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction HKL-2000 data scaling PHASER phasing Coot model building