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Crystal structure of S-adenosylmethionine tRNA ribosyltransferase (TM0574) from Thermotoga maritima at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 295 0.10M NP_Citrate 1, 4.0% NP_Peg 6000, % NP_PEG 4000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 295K 2 VAPOR DIFFUSION,SITTING DROP,NANODROP 293 0.10M NP_Citrate 2, 12.0% NP_PEG 4000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.98 58.78 3.66 66.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.033 α = 90 b = 122.843 β = 90 c = 131.207 γ = 90
Symmetry Space Group I 2 2 2
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 2003-10-18 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD APS 2003-08-06 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2 2 SYNCHROTRON APS BEAMLINE 19-ID 0.97934,1.00800,0.97921 APS 19-ID
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 2 29.39 100 0.073 14.8 7.3 65036 44.87
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 2 2.11 100 0.678 2.7 6.4 9393
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 29.39 61756 3280 99.94 0.18107 0.17951 0.1883 0.21041 0.2157 RANDOM 32.15
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] -2.08 1.47 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.747 r_dihedral_angle_4_deg 15.993 r_dihedral_angle_3_deg 14.577 r_scangle_it 7.898 r_dihedral_angle_1_deg 6.183 r_scbond_it 5.39 r_mcangle_it 3.29 r_mcbond_it 2.294 r_angle_refined_deg 1.529 r_angle_other_deg 0.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.747 r_dihedral_angle_4_deg 15.993 r_dihedral_angle_3_deg 14.577 r_scangle_it 7.898 r_dihedral_angle_1_deg 6.183 r_scbond_it 5.39 r_mcangle_it 3.29 r_mcbond_it 2.294 r_angle_refined_deg 1.529 r_angle_other_deg 0.805 r_mcbond_other 0.652 r_symmetry_vdw_other 0.287 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.192 r_nbd_other 0.19 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.092 r_nbtor_other 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4501 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 18
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling SOLVE phasing RESOLVE model building REFMAC refinement CCP4 data scaling RESOLVE phasing