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Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum (Hexagonal P form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9YRU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. Crystals were obtained as the GSU complex and soaked for 2 weeks with 10 mM Histidine in cryoprotectant. This displaced the GSU ligand resulting in an apo structure. Histidine was not bound. plate Liu-S-192 H8 , Puck: PSL-0115, Cryo: 3.4M sodium malonate
Crystal Properties Matthews coefficient Solvent content 3.47 64.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.174 α = 90 b = 120.174 β = 90 c = 363.17 γ = 120
Symmetry Space Group P 61 2 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 PIXEL DECTRIS EIGER2 XE 9M 2025-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.87 50.02 100 0.23 0.233 0.037 0.999 20.4 38.8 36614
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.87 2.94 100 3.959 4.006 0.611 0.638 41.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.87 47.81 1.34 36503 1738 99.95 0.2164 0.2154 0.2151 0.236 0.2375
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.446 f_angle_d 0.563 f_chiral_restr 0.042 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7045 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction