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heterotetrameric glycyl-tRNA synthetase from Escherichia coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 291 0.4 M magnesium acetate, 0.1 M HEPES pH 6.8, 2% (v/v) PEG 3350, 2% (v/v) PEG 5000 MME, 2% (v/v) PEG 4000, 2% (v/v) PEG 2000 and 10% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 4.47 72.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 207.371 α = 90 b = 253.945 β = 90 c = 270.738 γ = 90
Symmetry Space Group F 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 PIXEL DECTRIS PILATUS3 6M 2019-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97918 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.68 50 100 0.084 0.087 0.024 9.4 13.5 99458
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.68 2.78 100 0.602 0.627 0.173 0.963 13.1
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 SAD THROUGHOUT 2.68 48.58 94460 4996 99.78 0.2293 0.2282 0.2339 0.2487 0.2551 RANDOM 68.394
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] -0.17 -4.98 5.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.946 r_dihedral_angle_4_deg 15.958 r_dihedral_angle_3_deg 15.268 r_dihedral_angle_1_deg 5.584 r_angle_other_deg 2.285 r_angle_refined_deg 1.21 r_chiral_restr 0.041 r_bond_other_d 0.035 r_gen_planes_other 0.004 r_bond_refined_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.946 r_dihedral_angle_4_deg 15.958 r_dihedral_angle_3_deg 15.268 r_dihedral_angle_1_deg 5.584 r_angle_other_deg 2.285 r_angle_refined_deg 1.21 r_chiral_restr 0.041 r_bond_other_d 0.035 r_gen_planes_other 0.004 r_bond_refined_d 0.003 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13251 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction CRANK2 phasing