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CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum / Plasmodium falciparum chimera COMPLEXED WITH L-LYSINE AND INHIBITOR DDD02174286
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ELO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293 Protein: 30 mg/ml in 25 mM HEPES, 0.5 M NaCl, 5 % glycerol, 2 mM TCEP, pH 7, 5 mM lysine
Reservoir: 25% PEG 3350, 0.2 M Li sulfate, 0.1 M tris pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.47 50.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.808 α = 90 b = 116.579 β = 90 c = 142.991 γ = 90
Symmetry Space Group P 2 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 2020-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.9 61.83 100 0.162 0.065 0.998 12.8 13.7 96515
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.949 99.7 1.668 0.662 0.685 2 14
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 61.83 96445 4822 99.943 0.162 0.16 0.1706 0.1897 0.1978 23.76
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] -0.292 0.944 -0.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.1 r_dihedral_angle_3_deg 12.611 r_dihedral_angle_2_deg 8.669 r_dihedral_angle_1_deg 6.706 r_lrange_it 6.489 r_lrange_other 6.425 r_scangle_other 5.148 r_scangle_it 5.147 r_scbond_it 3.362 r_scbond_other 3.362
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.1 r_dihedral_angle_3_deg 12.611 r_dihedral_angle_2_deg 8.669 r_dihedral_angle_1_deg 6.706 r_lrange_it 6.489 r_lrange_other 6.425 r_scangle_other 5.148 r_scangle_it 5.147 r_scbond_it 3.362 r_scbond_other 3.362 r_mcangle_it 3.115 r_mcangle_other 3.115 r_mcbond_it 2.231 r_mcbond_other 2.231 r_angle_refined_deg 1.678 r_dihedral_angle_other_2_deg 0.641 r_angle_other_deg 0.573 r_nbd_refined 0.215 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.181 r_nbd_other 0.172 r_symmetry_nbd_refined 0.147 r_xyhbond_nbd_refined 0.144 r_symmetry_xyhbond_nbd_refined 0.141 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_1 0.07 r_chiral_restr_other 0.026 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8059 Nucleic Acid Atoms Solvent Atoms 854 Heterogen Atoms 137
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing