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Terminal uridylyl transferase 4 from Trypanosoma brucei with bound UPU
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IKF pdb entry 2IKF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 100 mM sodium cacodylate, 200 mM calcium acetate, 18% PEG-8000, 4 mM MgCl2, 50 uM UTP, crystals soaked in 10 mM UPU for 30 minutes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.27 45.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.544 α = 90 b = 41.953 β = 95.62 c = 106.593 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 2006-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.979 SSRL BL9-1
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 2.3 46.53 99.9 0.141 5.6 3.65 32493
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) 2.3 2.38 100 0.52 2.1 3.68 3199
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2IKF 2.3 46.52 32469 1681 99.86 0.231 0.228 0.227 0.296 0.2972 test set taken from 2IKF 44.789
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] 0.08 0.17 -0.07 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.333 r_dihedral_angle_3_deg 19.281 r_dihedral_angle_4_deg 17.443 r_dihedral_angle_1_deg 6.522 r_scangle_it 2.569 r_scbond_it 1.65 r_angle_refined_deg 1.608 r_mcangle_it 1.289 r_mcbond_it 0.727 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.333 r_dihedral_angle_3_deg 19.281 r_dihedral_angle_4_deg 17.443 r_dihedral_angle_1_deg 6.522 r_scangle_it 2.569 r_scbond_it 1.65 r_angle_refined_deg 1.608 r_mcangle_it 1.289 r_mcbond_it 0.727 r_nbtor_refined 0.304 r_xyhbond_nbd_refined 0.215 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.205 r_symmetry_hbond_refined 0.181 r_metal_ion_refined 0.136 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5174 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 78
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection d*TREK data reduction PHASER phasing