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High resolution crystal structure of an editosome enzyme from trypanosoma brucei: RNA editing ligase 1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 PEG 3350, magnesium chloride, Tris, ATP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.3 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.911 α = 90 b = 58.579 β = 100.23 c = 52.984 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 100 CCD ADSC QUANTUM 4 2003-12-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97885, 0.97899, 0.96112 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.1 50 86.8 0.064 0.064 33.8 95711 2 7.293
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 86.8 0.064 0.064 33.8 95711
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.2 20 78835 4149 98.3 0.12923 0.12822 0.1286 0.14805 0.1455 RANDOM 9.403
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] -0.22 0.12 -0.02 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.763 r_scangle_it 4.258 r_scbond_it 2.829 r_mcangle_it 1.915 r_angle_refined_deg 1.42 r_mcbond_it 1.192 r_angle_other_deg 0.784 r_nbd_other 0.25 r_nbd_refined 0.22 r_symmetry_vdw_other 0.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.763 r_scangle_it 4.258 r_scbond_it 2.829 r_mcangle_it 1.915 r_angle_refined_deg 1.42 r_mcbond_it 1.192 r_angle_other_deg 0.784 r_nbd_other 0.25 r_nbd_refined 0.22 r_symmetry_vdw_other 0.217 r_symmetry_hbond_refined 0.177 r_xyhbond_nbd_refined 0.169 r_symmetry_vdw_refined 0.119 r_chiral_restr 0.084 r_nbtor_other 0.084 r_gen_planes_other 0.017 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 2119 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing