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Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.8 pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.8 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.047 α = 90 b = 81.047 β = 90 c = 140.893 γ = 120
Symmetry Space Group P 32 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 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.00798, 0.97788, 0.97788, 0.95372 ESRF BM14
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 2.5 25 96.1 0.075 22.7 8.5 18357
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) 1 2.5 2.57 82 0.57 1.9 5.3
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 2.5 24.91 17240 915 98.9 0.229 0.227 0.2254 0.278 0.2782 RANDOM 58.61
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] 2.48 1.24 2.48 -3.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.912 r_dihedral_angle_3_deg 16.835 r_dihedral_angle_4_deg 16.51 r_dihedral_angle_1_deg 5.824 r_scangle_it 4.586 r_scbond_it 2.954 r_mcangle_it 1.225 r_angle_refined_deg 1.191 r_mcbond_it 0.716 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.912 r_dihedral_angle_3_deg 16.835 r_dihedral_angle_4_deg 16.51 r_dihedral_angle_1_deg 5.824 r_scangle_it 4.586 r_scbond_it 2.954 r_mcangle_it 1.225 r_angle_refined_deg 1.191 r_mcbond_it 0.716 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.214 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.08 r_bond_refined_d 0.009 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2964 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling