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CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01932549
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 2.49 50.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.152 α = 90 b = 116.852 β = 90 c = 143.262 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 CCD RIGAKU SATURN 944+ 2019-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5417
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 46.924 99.1 0.174 0.066 0.985 10.1 13.5 54785
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.37 96.9 0.414 0.208 0.957 3.7 9.1
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 2.3 46.924 54729 2695 98.896 0.216 0.2137 0.2184 0.2612 0.2639 14.704
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] -0.87 1.03 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.98 r_dihedral_angle_3_deg 13.068 r_dihedral_angle_2_deg 8.296 r_dihedral_angle_1_deg 6.992 r_lrange_it 4.913 r_lrange_other 4.781 r_scangle_other 3.451 r_scangle_it 3.45 r_mcangle_it 2.481 r_mcangle_other 2.481
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.98 r_dihedral_angle_3_deg 13.068 r_dihedral_angle_2_deg 8.296 r_dihedral_angle_1_deg 6.992 r_lrange_it 4.913 r_lrange_other 4.781 r_scangle_other 3.451 r_scangle_it 3.45 r_mcangle_it 2.481 r_mcangle_other 2.481 r_scbond_other 2.127 r_scbond_it 2.126 r_angle_refined_deg 1.673 r_mcbond_it 1.543 r_mcbond_other 1.543 r_dihedral_angle_other_2_deg 0.976 r_angle_other_deg 0.578 r_nbd_refined 0.21 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.178 r_xyhbond_nbd_refined 0.175 r_nbd_other 0.169 r_symmetry_xyhbond_nbd_other 0.113 r_symmetry_nbd_refined 0.107 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_1 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8053 Nucleic Acid Atoms Solvent Atoms 796 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building