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Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.6 A resolution with 1-METHYLQUINOLIN-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 2.63 53.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.827 α = 90 b = 75.351 β = 90.01 c = 87.048 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 MARRESEARCH 2005-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL1-5 0.92014 SSRL BL1-5
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 95.64 0.049 11 2.3 46217 15.665
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 92.53 0.165 2.2 2.2 6400
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 46217 2484 95.64 0.1663 0.1663 0.1652 0.1787 0.18712 0.1841 RANDOM 13.735
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] -0.01 0.04 -0.04 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.509 r_dihedral_angle_4_deg 15.864 r_dihedral_angle_3_deg 10.64 r_dihedral_angle_1_deg 4.869 r_scangle_it 3.146 r_scbond_it 2.203 r_mcangle_it 1.486 r_mcbond_it 1.437 r_angle_refined_deg 0.934 r_angle_other_deg 0.728
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.509 r_dihedral_angle_4_deg 15.864 r_dihedral_angle_3_deg 10.64 r_dihedral_angle_1_deg 4.869 r_scangle_it 3.146 r_scbond_it 2.203 r_mcangle_it 1.486 r_mcbond_it 1.437 r_angle_refined_deg 0.934 r_angle_other_deg 0.728 r_mcbond_other 0.241 r_symmetry_vdw_other 0.24 r_nbd_refined 0.213 r_nbtor_refined 0.182 r_nbd_other 0.166 r_symmetry_vdw_refined 0.1 r_xyhbond_nbd_refined 0.097 r_symmetry_hbond_refined 0.088 r_nbtor_other 0.081 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 374 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing