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Crystal structure of Tryptophanyl-tRNA synthetase from Elizabethkingia anophelis NUHP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TZL PDB entry 3TZL as per MoRDa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 22.6 mg/mL ElanA.00743.a.B1.PS38400 + Molecular Dimensions Morpheus screen, condition C10 (10% w/v PEG8000, 20% v/v ethylene glycol, 30 mM each NPS, 100 mM bicine/Trizma base, pH 8.5, sodium nitrate, 0.3 M disodium hydrogen phosphate, 0.3 M ammonium sulfate), cryoprotectant: direct, Tray 299155c10, puck OVZ1-7
Crystal Properties Matthews coefficient Solvent content 2.17 43.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.07 α = 90 b = 105.92 β = 90 c = 94.19 γ = 90
Symmetry Space Group C 2 2 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+ 2018-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 47.095 99.3 0.041 0.043 0.999 33.22 12.517 22221 45.669
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99.9 0.507 0.54 0.95 4.19 8.363
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3TZL as per MoRDa 2 47.095 1.34 22197 1936 99.24 0.204 0.1998 0.2028 0.2451 0.2469 0 50.5227
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 13.068 f_angle_d 0.768 f_chiral_restr 0.047 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2394 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing ARP/wARP model building Coot model building