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Thermus thermophilus asparaginyl-tRNA synthetase with bound sulphamoyl-analogue of asparaginyl-adenylate (AsnAMS)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Native asparaginyl-tRNA synthetase structures
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 Native crystals grown with protein 5 mg ml- l, 12-15 % PEG 6000, 0.3M KCI at pH 8.4.
Soaked for 15 h in mother liquor containing 100 mM AsnAMS.
Crystal Properties Matthews coefficient Solvent content 2.81 56.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.183 α = 90 b = 125.183 β = 90 c = 126.591 γ = 120
Symmetry Space Group P 64 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 IMAGE PLATE MAR scanner 300 mm plate 1997-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.890 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 2.62 14.84 94.5 0.052 9.54 7.1 16965
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 2.62 2.69 0.257
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.62 14.84 16962 1717 93.352 0.215 0.209 0.209 0.2726 0.2726 57.357
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] -1.168 -0.584 -1.168 3.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.893 r_dihedral_angle_6_deg 10.604 r_lrange_it 6.843 r_dihedral_angle_1_deg 5.941 r_scangle_it 4.006 r_dihedral_angle_2_deg 3.576 r_mcangle_it 3.553 r_scbond_it 2.358 r_mcbond_it 2.09 r_angle_refined_deg 1.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.893 r_dihedral_angle_6_deg 10.604 r_lrange_it 6.843 r_dihedral_angle_1_deg 5.941 r_scangle_it 4.006 r_dihedral_angle_2_deg 3.576 r_mcangle_it 3.553 r_scbond_it 2.358 r_mcbond_it 2.09 r_angle_refined_deg 1.061 r_nbtor_refined 0.301 r_nbd_refined 0.185 r_symmetry_nbd_refined 0.116 r_xyhbond_nbd_refined 0.11 r_chiral_restr 0.084 r_symmetry_xyhbond_nbd_refined 0.056 r_gen_planes_refined 0.003 r_bond_refined_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3593 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing