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Crystal structure of Histidine--tRNA ligase from Elizabethkingia sp. CCUG 26117
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B26 PDB entries 3netA_1, 4g84A_2, 6b26A_1 as per Morda experimental model PDB 3NET PDB entries 3netA_1, 4g84A_2, 6b26A_1 as per Morda experimental model PDB 4G84 PDB entries 3netA_1, 4g84A_2, 6b26A_1 as per Morda
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 Microlytic MCSG1 condition E12: 2400mM Sodium malonate dibasic pH 7.0: ElmeA.00686.a.B1.PW38399 at 19.3mg/ml: cryo: direct: tray 299159e12: puck dod0-8
Crystal Properties Matthews coefficient Solvent content 2.7 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.8 α = 90 b = 68.56 β = 118.66 c = 97.22 γ = 90
Symmetry Space Group C 1 2 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 RAYONIX MX-300 2018-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.1 47.895 97.8 0.059 0.07 0.997 13.86 3.457 31772 37.268
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 2.1 2.15 86.2 0.337 0.438 0.863 2.58 2.343
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entries 3netA_1, 4g84A_2, 6b26A_1 as per Morda 2.1 47.895 1.36 31762 1955 98 0.1744 0.1711 0.1738 0.225 0.2287 37.2869
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 14.831 f_angle_d 0.818 f_chiral_restr 0.048 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3454 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing PHASER phasing PARROT phasing Coot model building