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Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.6 A resolution with BENZO[CD]INDOL-2(1H)-ONE 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 4.6 277 30 % PEG MME 2000, 0.2 ammonium sulfate, 0.1 sodium acetate trihydrate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.57 52.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.928 α = 90 b = 75.513 β = 90.01 c = 86.336 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 2005-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 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 1.6 30 89.94 0.094 7.8 3.5 42601 20.35
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 1.6 1.686 55.95 0.282 2.5 2.6 3828
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2A0K 1.6 30 42601 2251 89.94 0.17926 0.17926 0.17779 0.1812 0.20777 0.176 RANDOM 20.065
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 0.02 -0.01 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.053 r_dihedral_angle_4_deg 16.353 r_dihedral_angle_3_deg 11.059 r_dihedral_angle_1_deg 4.937 r_scangle_it 3.763 r_scbond_it 2.652 r_mcangle_it 1.949 r_mcbond_it 1.717 r_angle_refined_deg 1.026 r_xyhbond_nbd_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.053 r_dihedral_angle_4_deg 16.353 r_dihedral_angle_3_deg 11.059 r_dihedral_angle_1_deg 4.937 r_scangle_it 3.763 r_scbond_it 2.652 r_mcangle_it 1.949 r_mcbond_it 1.717 r_angle_refined_deg 1.026 r_xyhbond_nbd_refined 0.31 r_nbtor_refined 0.306 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.126 r_symmetry_hbond_refined 0.087 r_chiral_restr 0.068 r_bond_refined_d 0.008 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 302 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing