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Crystal structure of the N-terminal anticodon-binding domain of non-discriminating aspartyl-tRNA synthetase from Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C0A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 7% (w/v) PEG 4000, 0.1 M ammonium sulfate, 0.1 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.62 57.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.83 α = 90 b = 61.83 β = 90 c = 141.376 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD RAYONIX MX-300 2013-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
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 30 98.9 0.057 27.2 5 19187
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 2.07 93.8 0.42 3.9 4.5
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 FREE R-VALUE 1C0A 2 27.65 18167 985 98.97 0.1814 0.18 0.1905 0.207 0.2172 RANDOM 33.408
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] 0.18 0.18 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.026 r_dihedral_angle_3_deg 13.165 r_dihedral_angle_4_deg 10.625 r_dihedral_angle_1_deg 6.537 r_mcangle_it 2.603 r_mcbond_it 1.687 r_mcbond_other 1.673 r_angle_refined_deg 1.253 r_angle_other_deg 0.692 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.026 r_dihedral_angle_3_deg 13.165 r_dihedral_angle_4_deg 10.625 r_dihedral_angle_1_deg 6.537 r_mcangle_it 2.603 r_mcbond_it 1.687 r_mcbond_other 1.673 r_angle_refined_deg 1.253 r_angle_other_deg 0.692 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1608 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing