☰ Navigation Tabs
CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01887015
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
Reservoir: 25% PEG 3350, 0.1 M tris pH 7.8, 0.2 M Li sulfate
Crystal Properties Matthews coefficient Solvent content 2.54 51.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.153 α = 90 b = 119.425 β = 90.308 c = 142.76 γ = 90
Symmetry Space Group P 1 21 1
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+ 2019-05-08 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 1.9 142.76 97.3 0.093 0.055 0.997 11.8 6.9 187306 18.767
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 1.9 1.93 90 0.658 0.514 0.706
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 91.768 187254 9337 97.166 0.181 0.1802 0.1886 0.2064 0.2118 21.331
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] -0.439 -0.495 1.227 -0.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.82 r_dihedral_angle_3_deg 12.113 r_dihedral_angle_2_deg 8.445 r_dihedral_angle_1_deg 6.82 r_lrange_it 5.613 r_lrange_other 5.558 r_scangle_it 4.493 r_scangle_other 4.491 r_scbond_it 2.87 r_scbond_other 2.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.82 r_dihedral_angle_3_deg 12.113 r_dihedral_angle_2_deg 8.445 r_dihedral_angle_1_deg 6.82 r_lrange_it 5.613 r_lrange_other 5.558 r_scangle_it 4.493 r_scangle_other 4.491 r_scbond_it 2.87 r_scbond_other 2.866 r_mcangle_it 2.641 r_mcangle_other 2.64 r_mcbond_it 1.851 r_mcbond_other 1.85 r_angle_refined_deg 1.543 r_angle_other_deg 0.522 r_nbd_refined 0.209 r_nbd_other 0.197 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.172 r_symmetry_nbd_refined 0.157 r_xyhbond_nbd_refined 0.138 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.066 r_ncsr_local_group_4 0.057 r_ncsr_local_group_6 0.057 r_ncsr_local_group_3 0.053 r_ncsr_local_group_1 0.045 r_ncsr_local_group_2 0.045 r_ncsr_local_group_5 0.039 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16196 Nucleic Acid Atoms Solvent Atoms 1376 Heterogen Atoms 255
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building