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The crystal structure of a human glycyl-tRNA synthetase mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other The native T.thermophilus GlyRS structure
Crystallization Crystal Properties Matthews coefficient Solvent content 3.32 62.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.412 α = 90 b = 91.412 β = 90 c = 246.814 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 CCD MARMOSAIC 325 mm CCD 2006-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.9795 SSRL BL9-1
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 2.85 50 99.1 0.066 15 13.8 25080
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 2.85 2.95 98.5 0.37 14 2419
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 The native T.thermophilus GlyRS structure 2.85 29.24 24999 1272 98.86 0.233 0.231 0.2241 0.271 0.2594 RANDOM 60.094
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] -0.05 -0.05 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.665 r_dihedral_angle_3_deg 15.962 r_dihedral_angle_4_deg 14.902 r_mcangle_it 7.074 r_dihedral_angle_1_deg 6.719 r_scangle_it 4.904 r_mcbond_it 4.783 r_scbond_it 3.341 r_angle_refined_deg 0.847 r_symmetry_hbond_refined 0.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.665 r_dihedral_angle_3_deg 15.962 r_dihedral_angle_4_deg 14.902 r_mcangle_it 7.074 r_dihedral_angle_1_deg 6.719 r_scangle_it 4.904 r_mcbond_it 4.783 r_scbond_it 3.341 r_angle_refined_deg 0.847 r_symmetry_hbond_refined 0.335 r_nbtor_refined 0.326 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.199 r_chiral_restr 0.078 r_bond_refined_d 0.003 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4144 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 7
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction