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Crystal structure of aspartyl-tRNA synthetase from Mycobacterium smegmatis with bound aspartic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EQR PDB ENTRY 1EQR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 289 20% PEG 3350, 0.2M Na Citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.04 59.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.4 α = 90 b = 135.17 β = 90 c = 157.05 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX300HE 2013-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.6 42.72 99.8 0.072 23.9 5.8 51452 51363 35.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.67 99.9 0.499 4.5 6 3761
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 1EQR 2.6 42.72 48854 2559 99.83 0.19785 0.19548 0.1997 0.24361 0.2458 RANDOM 49.356
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] 2.21 1.52 -3.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.649 r_dihedral_angle_4_deg 17.526 r_dihedral_angle_3_deg 13.733 r_dihedral_angle_1_deg 7.121 r_long_range_B_refined 4.675 r_long_range_B_other 4.675 r_mcangle_other 2.414 r_mcangle_it 2.413 r_scangle_other 2.397 r_angle_refined_deg 1.594
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.649 r_dihedral_angle_4_deg 17.526 r_dihedral_angle_3_deg 13.733 r_dihedral_angle_1_deg 7.121 r_long_range_B_refined 4.675 r_long_range_B_other 4.675 r_mcangle_other 2.414 r_mcangle_it 2.413 r_scangle_other 2.397 r_angle_refined_deg 1.594 r_scbond_it 1.535 r_scbond_other 1.533 r_mcbond_it 1.449 r_mcbond_other 1.437 r_angle_other_deg 1 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8163 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 50
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling