☰ Navigation Tabs
The crystal structure of MetRS-like protein from Streptomyces candidus in complex with L-Glu and L-N6-OH-lysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DLP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 100mm Tris ph8.5, 200 mM MgCl2, 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.24 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.583 α = 90 b = 50.534 β = 89.819 c = 106.613 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 PIXEL DECTRIS PILATUS 300K 2025-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CAMD BEAMLINE GCPCC 0.9786 CAMD GCPCC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.45 41.671 97.67 0.937 6.68 6.68 40316
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.51 0.937
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 NONE 2.45001012437 41.670422965 1.34982315741 40230 2021 99.5718139742 0.17461435973 0.172299418746 0.1808 0.217855203499 0.2201 20.2396439714
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 14.6504850803 f_angle_d 1.28992055099 f_chiral_restr 0.0532522755995 f_bond_d 0.0133244504068 f_plane_restr 0.00749687534746
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8229 Nucleic Acid Atoms Solvent Atoms 668 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing Coot model building