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Crystal structure of E. coli heterotetrameric GlyRS in complex with tRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EIV 7eiv, 4mgm experimental model PDB 4MGM 7eiv, 4mgm
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 0.15M MgCl2, 0.1M NaCl, 0.1M Tris-HCl pH 8.5, 30% PEG 300
Crystal Properties Matthews coefficient Solvent content 3.73 67.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.71 α = 90 b = 162.123 β = 90 c = 324.09 γ = 90
Symmetry Space Group P 2 2 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 PIXEL DECTRIS EIGER X 16M 2021-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.907 162.12 100 0.138 0.059 0.99 9.4 6.6 85473
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.907 3.06 0.749 0.304 0.774
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7eiv, 4mgm 2.907 50.005 85392 4393 99.885 0.231 0.2296 0.2337 0.2598 0.263 77.244
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] 6.585 -2.903 -3.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.037 r_dihedral_angle_4_deg 18.004 r_dihedral_angle_3_deg 16.983 r_lrange_it 5.745 r_lrange_other 5.745 r_dihedral_angle_1_deg 5.556 r_scangle_it 3.494 r_scangle_other 3.493 r_mcangle_other 3.475 r_mcangle_it 3.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.037 r_dihedral_angle_4_deg 18.004 r_dihedral_angle_3_deg 16.983 r_lrange_it 5.745 r_lrange_other 5.745 r_dihedral_angle_1_deg 5.556 r_scangle_it 3.494 r_scangle_other 3.493 r_mcangle_other 3.475 r_mcangle_it 3.474 r_mcbond_it 2.073 r_mcbond_other 2.073 r_scbond_it 2.068 r_scbond_other 2.068 r_angle_refined_deg 1.231 r_angle_other_deg 1.171 r_symmetry_nbd_other 0.193 r_nbd_refined 0.184 r_nbd_other 0.173 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.097 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_other 0.06 r_symmetry_nbd_refined 0.059 r_chiral_restr 0.051 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14340 Nucleic Acid Atoms 2952 Solvent Atoms 14 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling MOLREP phasing