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Crystal Structure of a parasite tRNA synthetase, ligand-free
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HV0 PDB ENTRY 3HV0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2 M sodium citrate, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.06 59.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.301 α = 90 b = 190.669 β = 90 c = 51.732 γ = 90
Symmetry Space Group P 21 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 315r 2010-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 ALS 5.0.2
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 2.34 50 100 0.088 11.5 7.3 49735
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 2.34 2.38 100 0.363 6.5 2412
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 3HV0 2.34 30 49504 2506 99.42 0.1808 0.1793 0.1827 0.2094 0.2112 RANDOM 45.8473
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] -0.12 -0.03 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.162 r_dihedral_angle_4_deg 16.013 r_dihedral_angle_3_deg 12.586 r_dihedral_angle_1_deg 5.51 r_angle_refined_deg 1.077 r_mcangle_it 1.005 r_angle_other_deg 0.843 r_mcbond_it 0.585 r_mcbond_other 0.584 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.162 r_dihedral_angle_4_deg 16.013 r_dihedral_angle_3_deg 12.586 r_dihedral_angle_1_deg 5.51 r_angle_refined_deg 1.077 r_mcangle_it 1.005 r_angle_other_deg 0.843 r_mcbond_it 0.585 r_mcbond_other 0.584 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5959 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction