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Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.7 A resolution with 5-Aminoisoquinoline bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A0K pdb entry 2A0K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 30 % PEG MME 2000
0.2 ammonium sulfate
0.1 sodium acetate trihydrate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.57 52.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.96 α = 90 b = 75.493 β = 90.05 c = 86.324 γ = 90
Symmetry Space Group C 1 2 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 2005-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.92020 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 30 92.83 0.066 10.7 3.1 36740 18.141
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.792 67.24 0.217 3.9 2.2 3881
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 (All) 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 2A0K 1.7 30 36740 1928 92.83 0.17794 0.17794 0.17656 0.20373 0.2052 RANDOM 13.905
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] -0.07 -0.11 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.344 r_dihedral_angle_4_deg 14.392 r_dihedral_angle_3_deg 10.424 r_dihedral_angle_1_deg 4.655 r_scangle_it 2.562 r_scbond_it 1.735 r_mcangle_it 1.325 r_mcbond_it 1.155 r_angle_refined_deg 0.863 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.344 r_dihedral_angle_4_deg 14.392 r_dihedral_angle_3_deg 10.424 r_dihedral_angle_1_deg 4.655 r_scangle_it 2.562 r_scbond_it 1.735 r_mcangle_it 1.325 r_mcbond_it 1.155 r_angle_refined_deg 0.863 r_nbtor_refined 0.301 r_symmetry_hbond_refined 0.229 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.129 r_xyhbond_nbd_refined 0.077 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 2518 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing