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Crystal structure of apo-wildtype Glycyl-tRNA synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ATI PDB entry 1ATI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 20% PEG 3350, 0.2M Sodium bromide, 0.1M Bis-Tris propane, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.37 63.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.53 α = 90 b = 92.53 β = 90 c = 246.86 γ = 90
Symmetry Space Group P 43 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 100 CCD ADSC QUANTUM 4 MIRRORS 2005-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.93300 ESRF ID14-2
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 3 30 95.6 0.186 10.3 9.2 21172
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 3 3.11 90 0.986 1.8 8 1941
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 1ATI 3 29.27 20082 1021 94.6 0.20749 0.20526 0.2084 0.25013 0.2502 RANDOM 31.316
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] 0.3 0.3 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.579 r_dihedral_angle_4_deg 16.713 r_dihedral_angle_3_deg 16.347 r_scangle_it 7.564 r_dihedral_angle_1_deg 5.722 r_scbond_it 5.095 r_mcangle_it 3.966 r_mcbond_it 2.877 r_angle_refined_deg 1.004 r_angle_other_deg 0.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.579 r_dihedral_angle_4_deg 16.713 r_dihedral_angle_3_deg 16.347 r_scangle_it 7.564 r_dihedral_angle_1_deg 5.722 r_scbond_it 5.095 r_mcangle_it 3.966 r_mcbond_it 2.877 r_angle_refined_deg 1.004 r_angle_other_deg 0.773 r_mcbond_other 0.555 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.216 r_symmetry_vdw_other 0.185 r_nbd_other 0.181 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.099 r_symmetry_hbond_refined 0.084 r_nbtor_other 0.082 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4213 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling CNS phasing