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Crystal structure of the E.coli tRNAArg aminoacyl stem issoacceptor RR-1660 at 2.0 Angstroem resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VUQ PDB ENTRY 2VUQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 294 10 MM MAGNESIUM CHLORIDE, 50 MM MES, PH 5.6, 2 M LITHIUM SULFATE, 294K, CRYOPROTECTANT 20 % (V/V) GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.34 59.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.368 α = 105.89 b = 28.984 β = 98.76 c = 29.134 γ = 97.85
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 203 CCD MARRESEARCH 2008-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R ELETTRA 5.2R
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 1.7 40 95 0.04 22.2 1.8 7118 1.5
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 1.7 1.73 93.2 0.16 1.9 1.7
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 (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 2VUQ 2 20.92 5058 267 97.9 0.214 0.212 0.2157 0.255 0.192 RANDOM 26.21
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]
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.864 r_angle_refined_deg 2.567 r_scbond_it 2.282 r_nbtor_refined 0.27 r_xyhbond_nbd_refined 0.233 r_symmetry_hbond_refined 0.174 r_symmetry_vdw_refined 0.172 r_nbd_refined 0.169 r_chiral_restr 0.09 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.864 r_angle_refined_deg 2.567 r_scbond_it 2.282 r_nbtor_refined 0.27 r_xyhbond_nbd_refined 0.233 r_symmetry_hbond_refined 0.174 r_symmetry_vdw_refined 0.172 r_nbd_refined 0.169 r_chiral_restr 0.09 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_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_it r_mcbond_other r_mcangle_it 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 Nucleic Acid Atoms 586 Solvent Atoms 88 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing