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Crystal Structure of tetrameric form of human lysyl-tRNA synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E24 PDB entry 1E24
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.75 277 12% PEG8000, 16% Glycerol, 0.08M Na Cacodylate, 0.16M Ca(OAc)2, pH 5.75, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.01 59.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.013 α = 90 b = 152.013 β = 90 c = 108.838 γ = 120
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 300 mm CCD Si(111) Double Crystal
Monochrometer. Adjustable focusing mirrors in K-B geometry. 2007-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B APS 23-ID-B
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 2.1 40 98 0.097 5.7 1.6 160180
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) 2.1 2.18 98.2 0.53 0.87 1.6
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 1E24 2.31 25 114762 5985 98 0.197 0.194 0.1922 0.252 0.248 RANDOM 28.75
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] -1.21 -0.61 -1.21 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.339 r_dihedral_angle_4_deg 17.454 r_dihedral_angle_3_deg 16.43 r_dihedral_angle_1_deg 5.939 r_scangle_it 2.864 r_scbond_it 1.83 r_angle_refined_deg 1.313 r_mcangle_it 1.227 r_mcbond_it 0.759 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.339 r_dihedral_angle_4_deg 17.454 r_dihedral_angle_3_deg 16.43 r_dihedral_angle_1_deg 5.939 r_scangle_it 2.864 r_scbond_it 1.83 r_angle_refined_deg 1.313 r_mcangle_it 1.227 r_mcbond_it 0.759 r_nbtor_refined 0.323 r_symmetry_vdw_refined 0.257 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.223 r_symmetry_hbond_refined 0.207 r_metal_ion_refined 0.167 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16201 Nucleic Acid Atoms Solvent Atoms 1002 Heterogen Atoms 176
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction