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Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum bound to a difluoro cyclohexyl chromone ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H02
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.1 M Bis-Tris pH 6.5, 2 % (v/v) Tascimate pH 6.0, 20 % (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.14 42.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.137 α = 90 b = 95.344 β = 90 c = 166.517 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2017-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.074 ESRF ID29
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 1.62 83 99.9 0.062 10 4.3 148069
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.66 100 0.872 0.59 1.7 4.4
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 4H02 1.62 82.74 139948 7280 99.26 0.1848 0.1827 0.1936 0.226 0.2342 RANDOM 25.892
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] 0.35 0.53 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.035 r_dihedral_angle_4_deg 16.996 r_dihedral_angle_3_deg 14.301 r_dihedral_angle_1_deg 7.168 r_angle_refined_deg 2.245 r_angle_other_deg 1.181 r_chiral_restr 0.152 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.035 r_dihedral_angle_4_deg 16.996 r_dihedral_angle_3_deg 14.301 r_dihedral_angle_1_deg 7.168 r_angle_refined_deg 2.245 r_angle_other_deg 1.181 r_chiral_restr 0.152 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7860 Nucleic Acid Atoms Solvent Atoms 966 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction autoPROC data scaling MOLREP phasing