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Crystal structure of apo S581L Glycyl-tRNA synthetase mutant
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 6.5 293 20% PEG 3350, 0.2M Na2SO4, 0.1M Bis-Tris propane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.36 63.44
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 MARMOSAIC 225 mm CCD MIRRORS 2005-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97650 ESRF BM14
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 2.8 30 99.8 0.108 20.7 14.2 27432
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 2.8 2.9 98.5 0.734 1.5 5.9 2643
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 2.8 29.27 25923 1329 99.86 0.2144 0.21265 0.2163 0.24919 0.2481 RANDOM 34.963
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] 0.45 0.45 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.791 r_dihedral_angle_4_deg 15.649 r_dihedral_angle_3_deg 13.743 r_scangle_it 7.923 r_scbond_it 5.459 r_dihedral_angle_1_deg 5.159 r_mcangle_it 3.829 r_mcbond_it 2.996 r_angle_refined_deg 0.987 r_angle_other_deg 0.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.791 r_dihedral_angle_4_deg 15.649 r_dihedral_angle_3_deg 13.743 r_scangle_it 7.923 r_scbond_it 5.459 r_dihedral_angle_1_deg 5.159 r_mcangle_it 3.829 r_mcbond_it 2.996 r_angle_refined_deg 0.987 r_angle_other_deg 0.882 r_mcbond_other 0.581 r_symmetry_hbond_refined 0.26 r_nbd_refined 0.199 r_nbtor_refined 0.177 r_nbd_other 0.176 r_symmetry_vdw_refined 0.174 r_symmetry_vdw_other 0.174 r_chiral_restr 0.1 r_xyhbond_nbd_refined 0.092 r_nbtor_other 0.08 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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 4215 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling CNS phasing