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Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-lysine and a difluoro cyclohexyl chromone ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ELN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 25% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.63 53.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.514 α = 90 b = 142.65 β = 90 c = 72.939 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 PIXEL DECTRIS PILATUS 6M 2016-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.969 Diamond I24
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 1.46 73 97.6 0.076 10 5.6 205432
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 1.46 1.5 80.5 0.659 0.56 1.4 2.6
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 5ELN 1.46 72.94 194182 10237 97.14 0.1886 0.1872 0.1959 0.2149 0.2219 RANDOM 15.952
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] 0.7 -0.19 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.968 r_dihedral_angle_4_deg 14.52 r_dihedral_angle_3_deg 12.684 r_dihedral_angle_1_deg 6.716 r_angle_refined_deg 1.929 r_angle_other_deg 1.065 r_chiral_restr 0.124 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.968 r_dihedral_angle_4_deg 14.52 r_dihedral_angle_3_deg 12.684 r_dihedral_angle_1_deg 6.716 r_angle_refined_deg 1.929 r_angle_other_deg 1.065 r_chiral_restr 0.124 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8023 Nucleic Acid Atoms Solvent Atoms 907 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction xia2 data scaling MOLREP phasing