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Terminal uridylyl transferase 4 from Trypanosoma brucei with bound UTP and UMP
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 UMP for 30 minutes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.24 45.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.62 α = 90 b = 41.924 β = 94.37 c = 106.017 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 2006-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL1-5 0.979 SSRL BL1-5
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 2.4 41.92 93.8 0.14 6.4 3.38 26495
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) 2.4 2.49 93 0.476 2.3 3.48 2610
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 2.4 38.98 26486 1364 93.8 0.226 0.223 0.2213 0.293 0.2924 test set taken from 2IKF 41.465
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] 0.02 -0.02 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.658 r_dihedral_angle_4_deg 19.765 r_dihedral_angle_3_deg 19.004 r_dihedral_angle_1_deg 6.096 r_scangle_it 2.301 r_angle_refined_deg 1.553 r_scbond_it 1.436 r_mcangle_it 1.151 r_mcbond_it 0.654 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.658 r_dihedral_angle_4_deg 19.765 r_dihedral_angle_3_deg 19.004 r_dihedral_angle_1_deg 6.096 r_scangle_it 2.301 r_angle_refined_deg 1.553 r_scbond_it 1.436 r_mcangle_it 1.151 r_mcbond_it 0.654 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.171 r_symmetry_hbond_refined 0.133 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5132 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 73
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