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Terminal uridylyl transferase 4 from Trypanosoma brucei with bound ATP
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 ATP, 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 = 80.19 α = 90 b = 41.97 β = 94.01 c = 106.42 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 2006-07-04 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 42.87 99.5 0.092 8.5 3.56 48171
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 2.07 97.4 0.463 2.3 3.27 4646
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2IKF 2 35.38 48158 2473 99.45 0.222 0.221 0.254 0.2297 Test set taken from 2IKF 36.652
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] 0.39 0.24 -0.35 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.69 r_dihedral_angle_4_deg 18.428 r_dihedral_angle_3_deg 17.878 r_dihedral_angle_1_deg 6.179 r_scangle_it 3.237 r_scbond_it 2.12 r_angle_refined_deg 1.547 r_mcangle_it 1.516 r_mcbond_it 0.94 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.69 r_dihedral_angle_4_deg 18.428 r_dihedral_angle_3_deg 17.878 r_dihedral_angle_1_deg 6.179 r_scangle_it 3.237 r_scbond_it 2.12 r_angle_refined_deg 1.547 r_mcangle_it 1.516 r_mcbond_it 0.94 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.277 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5163 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 33
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection d*TREK data reduction CCP4 phasing